It's a constant leap frog scenario. Square Enix used to be king, but I don't see it as returning to any sort of stature any time soon. So it's between Bethesda and Bioware. Bioware has created some of the best games of all time, and so have Bethesda. I'm purely going on the fact that Bioware has made more good games than Bethesda. It's literally quantity over quality here, because their quality is equally matched.
They both have excellent standards. And I have no doubt that Bethesda will take the lead in my books when Skyrim comes out. But yeah, Enix, you don't stand a chance. The company has fallen into the realms of disappointment with me. All I do is forever long for them to return to what they used to do with a fresh new attitude. But no, they just make loads of run of the mill sci-fi high fantasy set in a unbelievable universe, littered with the most annoying characters I've ever seen in a game. And crap MMO's that just line this industry with fruitful failure stories.