MVP 06 is my favorite for Baseball Game of the Year in 2006. It looks like the most refreshing, and could have the best baseball engine if they make the right changes (which it sounds like they are). I gave MLB06 the award last year, but the new NCAA game looks like a big boost to the solid MVP series which ran second last year, and I expect the new batter/pitcher gameplay to rival MLB06 or even surpass it.
This should be the best MLB game however, unless like you said, 2K comes out of nowhere with an outstanding effort. I know Sony doubled the team of developers for this game compared to last year, and they carry the most momentum of any franchise.