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Obama stopped short of a veto threat on anti-LGBT provisions of NDAA.
But he objected to them, and they were removed before he signed it. Also, everything he threatened a veto over?
...We'll get there. Caution: lots to read below, and none of it particularly inflammatory. Sorry. 
Flashback to May 24, 2011: the President issues his Statement of Administration Policy on NDAA, outlining objections to the bill. PDF
STATEMENT OF ADMINISTRATION POLICY
H.R. 1540 – National Defense Authorization Act for FY 2012
(snip)
Military Regulations Regarding Marriage: The Administration strongly objects to sections 534 and 535, believes that section 3 of the so-called Defense of Marriage Act (DOMA) is discriminatory, and supports DOMA’s repeal.
H.R. 1540 – National Defense Authorization Act for FY 2012
(snip)
Military Regulations Regarding Marriage: The Administration strongly objects to sections 534 and 535, believes that section 3 of the so-called Defense of Marriage Act (DOMA) is discriminatory, and supports DOMA’s repeal.
Sections 534 and 535 read:
SEC. 534. MILITARY REGULATIONS REGARDING MARRIAGE.
Congress reaffirms the policy of section 3 of the Defense of Marriage Act, codified as section 7 of title 1, United States Code. In determining the meaning of any Act of Congress, or of any ruling, regulation, or interpretation of the Department of Defense applicable to members of the Armed Forces or civilian employees of the Department of Defense, the word `marriage' means only a legal union between one man and one woman as husband and wife, and the word `spouse' refers only to a person of the opposite sex who is a husband or a wife.
SEC. 535. USE OF MILITARY INSTALLATIONS AS SITE FOR MARRIAGE CEREMONIES AND PARTICIPATION OF CHAPLAINS AND OTHER MILITARY AND CIVILIAN PERSONNEL IN THEIR OFFICIAL CAPACITY.
(a) Limitation on Use- A military installation or other property under the jurisdiction of the Department of Defense may be used as the site for a marriage ceremony only if the marriage complies with the definition of marriage in section 7 of title 1, United States Code.
(b) Limitation on Participation- A member of the Armed Forces, including a chaplain, or civilian employee of the Department of Defense acting in an official capacity may assist in or perform a marriage ceremony only if the marriage complies with the definition of marriage in section 7 of title 1, United States Code.
Congress reaffirms the policy of section 3 of the Defense of Marriage Act, codified as section 7 of title 1, United States Code. In determining the meaning of any Act of Congress, or of any ruling, regulation, or interpretation of the Department of Defense applicable to members of the Armed Forces or civilian employees of the Department of Defense, the word `marriage' means only a legal union between one man and one woman as husband and wife, and the word `spouse' refers only to a person of the opposite sex who is a husband or a wife.
SEC. 535. USE OF MILITARY INSTALLATIONS AS SITE FOR MARRIAGE CEREMONIES AND PARTICIPATION OF CHAPLAINS AND OTHER MILITARY AND CIVILIAN PERSONNEL IN THEIR OFFICIAL CAPACITY.
(a) Limitation on Use- A military installation or other property under the jurisdiction of the Department of Defense may be used as the site for a marriage ceremony only if the marriage complies with the definition of marriage in section 7 of title 1, United States Code.
(b) Limitation on Participation- A member of the Armed Forces, including a chaplain, or civilian employee of the Department of Defense acting in an official capacity may assist in or perform a marriage ceremony only if the marriage complies with the definition of marriage in section 7 of title 1, United States Code.
These sections did not survive. Note: there was no veto threat, simply an objection.
Another objection made by this administration in May:
Attempts to Prevent, Delay, or Undermine the Repeal of "Don’t Ask, Don’t Tell": On December 22, 2010, President Obama signed into law the Don't Ask, Don't Tell Repeal Act of 2010, in order to strengthen our national security, enhance military readiness, and uphold the fundamental American principles of fairness and equality that warfighters defend around the world. As required by that statute, DoD is diligently working to prepare the necessary policies and regulations and conducting educational briefings to implement the repeal. Should it be determined, as required by the statute, that the implementation is consistent with the standards of military readiness and effectiveness, unit cohesion, and military recruiting and retention, then the President, the Secretary of Defense and the Chairman of the Joint Chiefs of Staff will send forward the required certification. The Administration strongly objects to any legislative attempts (such as section 533) to directly or indirectly undermine, prevent, or delay the implementation of the repeal, as such efforts create uncertainty for servicemembers and their families.
Section 533 read:
SEC. 533. ADDITIONAL CONDITION ON REPEAL OF DON'T ASK, DON'T TELL POLICY.
Effective as of December 22, 2010, and as if included therein as enacted, section 2(b) of Public Law 111-321 (124 Stat. 3516) is amended by adding at the end the following new paragraph:
`(3) The Chief of Staff of the Army, the Chief of Naval Operations, the Commandant of the Marine Corps, and the Chief of Staff of the Air Force each submit to the congressional defense committees the officer's written certification that repeal of section 654 of title 10, United States Code, will not degrade the readiness, effectiveness, cohesion, and morale of combat arms units and personnel of the Armed Force under the officer's jurisdiction engaged in combat, deployed to a combat theater, or preparing for deployment to a combat theater.'.
Effective as of December 22, 2010, and as if included therein as enacted, section 2(b) of Public Law 111-321 (124 Stat. 3516) is amended by adding at the end the following new paragraph:
`(3) The Chief of Staff of the Army, the Chief of Naval Operations, the Commandant of the Marine Corps, and the Chief of Staff of the Air Force each submit to the congressional defense committees the officer's written certification that repeal of section 654 of title 10, United States Code, will not degrade the readiness, effectiveness, cohesion, and morale of combat arms units and personnel of the Armed Force under the officer's jurisdiction engaged in combat, deployed to a combat theater, or preparing for deployment to a combat theater.'.
This section also did not survive. Note: again, there was no veto threat, simply an objection.
But what of this "promise to veto NDAA" everyone's talking about?? Where were the veto threats? Great question. Let's look, there were three:
F-35 Joint Strike Fighter Propulsion System: The Administration strongly objects to the language in section 215, which limits the obligation or expenditure of funds for performance improvements to the F-35 Lightning II propulsion system unless there is competitive development and production of such a propulsion system. As the test program unfolds, some improvements are likely to be needed. And this would result in the continued development of an extra engine that adds significant extra costs to the program for something the Administration and the Department of Defense (DoD) have determined is not needed and would destabilize the F-35 program when it is beginning to stabilize. Additionally, section 215 would delay development of the main engine and affect the viability of the short take off and vertical landing variant. If the final bill presented to the President includes funding or a legislative direction to continue an extra engine program, the President's senior advisors would recommend a veto.
Classic "inside baseball" DoD stuff. Lots to read on DU about it, but ultimately: This section also did not survive.
Next up:
Limitations on Nuclear Force Reductions and Nuclear Employment Strategy: The Administration strongly objects to sections 1055 and 1056, which impinge on the President’s authority to implement the New START Treaty and to set U.S. nuclear weapons policy. In particular, section 1055 would set onerous conditions on the Administration’s ability to implement the Treaty, as well as to retire, dismantle, or eliminate non-deployed nuclear weapons. Among these conditions is the completion and operation of the next generation of nuclear facilities, which is not expected until the mid-2020s. The effect of this section would be to preclude dismantlement of weapons in excess of military needs. Additionally, it would significantly increase stewardship and management costs and divert key resources from our critical stockpile sustainment efforts and delay completion of programs necessary to support the long-term safety, security, and reliability of our nuclear deterrent. Further, section 1056 raises constitutional concerns as it appears to encroach on the President’s authority as Commander in Chief to set nuclear employment policy – a right exercised by every president in the nuclear age from both parties. If the final bill presented to the President includes these provisions, the President's senior advisors would recommend a veto.
By now you know what's coming: These sections did not survive.
Here's the "big one" on DU at the moment:
Detainee Matters: The Administration strongly objects to section 1034 which, in purporting to affirm the conflict, would effectively recharacterize its scope and would risk creating confusion regarding applicable standards. At a minimum, this is an issue that merits more extensive consideration before possible inclusion. The Administration strongly objects to the provisions that limit the use of authorized funds to transfer detainees and otherwise restrict detainee transfers and to the provisions that would legislate Executive branch processes for periodic review of detainee status and regarding prosecution of detainees. Although the Administration opposes the release of detainees within the United States, Section 1039 is a dangerous and unprecedented challenge to critical Executive branch authority to determine when and where to prosecute detainees, based on the facts and the circumstances of each case and our national security interests. It unnecessarily constrains our Nation's counterterrorism efforts and would undermine our national security, particularly where our Federal courts are the best – or even the only – option for incapacitating dangerous terrorists. For decades, presidents of both political parties – including Presidents Ronald Reagan, George H.W. Bush, Bill Clinton, and George W. Bush – have leveraged the flexibility and strength of our Federal courts to incapacitate dangerous terrorists and gather critical intelligence. The prosecution of terrorists in Federal court is an essential element of our counterterrorism efforts – a powerful tool that must remain an available option. The certification requirement in section 1040, restricting transfers to foreign countries, interferes with the authority of the Executive branch to make important foreign policy and national security determinations regarding whether and under what circumstances such transfers should occur. The Administration must have the ability to act swiftly and to have broad flexibility in conducting its negotiations with foreign countries. Section 1036 undermines the system of periodic review established by the President’s March 7, 2011, Executive Order by substituting a rigid system of review that could limit the advice and expertise of critical intelligence and law enforcement professionals, undermining the Executive branch’s ability to ensure that these decisions are informed by all available information and protect the full spectrum of our national security interests. It also unnecessarily interferes with DoD’s ability to manage detention operations. Section 1042 is problematic and unnecessary, as there already is robust coordination between the Department of Justice, the Department of Defense, and the Intelligence Community on terrorism-related cases, and this provision would undermine, rather than enhance, this coordination by requiring institutions to assume unfamiliar roles and could cause delays in taking into custody individuals who pose imminent threats to the nation’s safety. If the final bill presented to the President includes these provisions that challenge critical Executive branch authority, the President’s senior advisors would recommend a veto.
So Section 1034's confusing "re-affirmation" of AUMF (which some, including clearly the President, believe was defanged by its own section (d) Senate amendment), the certification requirement in Section 1040 (gone), the new review system in Section 1036 (gone), and the re-shuffling of Section 1042 (gone). Those were the objections.
This post is too long by far already, so I'll stop here for now. But there's the new (to me, at least) story of some good done on DADT and DOMA matters, and the meat behind the notion of "Obama promised to veto NDAA."
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I can imagine all of them shuddering about the 24/7 headlines about Obama threatening to shut down the armed forces because of the "gay agenda." God forbid we have a decent civil rights discourse in this country around this issue. 
But you're right, it was probably advisers thinking first to protect the President, rather than thinking what would be best for the country -- especially knowing it could be a big enough issue to last through to the election. Weak sauce, by that measure.
Although. Only a handful of objections, and these were among them. I was happy to find them there, although I'd have been happier to find them among the veto threats.
Most important, though, was that they didn't find their way into law. Had Obama signed anything that delayed DADT or supported DOMA I'd have been much more disappointed. He protested, and got his way: the right way.
