I think the annoying thing isn't that the guy who gets top control usually wins, it's more that that judges seem to think that the guy who gets top control ALWAYS WINS. This rewards the takedown and top control too much and ignores how comfortable the guy on the bottom is and what he is doing. While GSP clearly won the fight, there is no way that he won every round.
The UFC markets itself as being "as real as it gets" and mixed martial arts get their legitimacy from how effective they are in real combat situations - therefore, the judging should be as close as possible to what would win a real fight - damage and closeness to getting the finish.
That said, I don't think lay and pray is that big a problem, just because guys who do it don't get many fans and therefore don't make much money.