... the histories of the companies are not quite what you describe. Both Exxon and Chevron ultimately go back to Rockefeller's Standard Oil, but the 1911 anti-trust suit which broke up Standard Oil created thirty-four different entities, one of which was Jersey Standard, which eventually became Exxon, and another, Standard Oil of California, eventually became Chevron. They have been separate companies under separate control since 1911, therefore, so it's a bit confusing to say "Chevron AKA Exxon."
Since Prescott Bush was working his trading with the enemy magic through Union Bank shortly before and during WWII, it's probably inappropriate to say simply that his boss was Standard Oil. Actually, the company implicated in the Trading With The Enemy Act violations was Standard Oil of New Jersey (Jersey Standard) and its subsidiary, the Ethyl Corporation.
I suspect that, because of the elder Bush's interests in Zapata, he's probably close to most of the people in the oil bidness, as they say in Texas, but probably more particularly with the Houston- and Dallas-based firms, of which UNOCAL is not one. Both Chevron and UNOCAL are originally (and still are) California companies.
The closest visible link between the current Bush and UNOCAL is Zalmay Khalilzad, and that link is a tenuous one. He actually worked for a firm which consulted to UNOCAL, rather than working for them directly, and then, not for very long. Khalilzad was far more involved in central Asian affairs at the State Dept. during the Reagan years, long before he ever did any consulting related to UNOCAL.
Hamid Karzai was a UNOCAL employee at one time, and that made him pliable and suitable for the administration's purposes, because he was reliably pro-US, but even that might not be directly related to petroleum company interests. In fact, Bush's hosting of the Taliban, when governor of Texas, may have had more to do with screwing an Argentinian company, Bridas, which had won a contract with the Afghani government in 1996 to build that very same pipeline in question, rather than due to some extraordinary closeness of the Bushes to UNOCAL:
http://www.worldpress.org/specials/pp/pipeline_timeline.htm Not saying that the Bushes don't look out for everybody in the oil business; it's just that there's no evidence I can find that they have extraordinary ties to UNOCAL beyond those with firms to which they would have been closer to, geographically, socially and economically, in Texas.
All that said, is this merger problematic? Yes, in the same way that any other merger with very large equals in the business leads to more layoffs and more anti-competitive behavior. The oil companies have consolidated much more power since the trust breakups of a century ago, and have acquired a lot more political power as a result. But, is this by design because of a closeness of the Bushes to UNOCAL? Not likely.
Cheers.