I've been spending time in some of the sports gaming forums (and yes, it makes me feel like I need a shower) to see how the reaction to MLB 2k9 has been thus far, and not surprisingly, people are all over the map with the game. You've gotta love it when you see a guy proclaiming it the best baseball evah, two posts away from someone proclaiming it the worst.
One thing I've noticed a lot of is people having trouble with the fielding. It's gratifying to know this isn't just me.
If the fielding is your biggest gripe with the game, I encourage you to hang in there. You can't get rid of every instance of on-field wonkiness with players not fielding balls despite being in position to do so, but as you get a feel for how the game controls the rate at which your fielder covers ground in the game and where you need to be to ensure you trigger an appropriate catch/pickup animation, you will be able to reduce these occurrences. Significantly.
There's also been a lot of people seeing issues with the first baseman pulling his foot off the bag for no good reason (in other words, the throw is on target and he still pulls his foot off). I have seen this, but in all the games I played it only happened twice. Both times when I had allowed the throw meter go into the red. In these cases it seems like the game wants there to be a throwing error, but for whatever reason doesn't generate a truly offline throw. Nevertheless the first baseman positions himself (or jumps) like the throw is too far off the bag. (This is just my theory.) Pretty lame, but if you avoid letting the throw meter go into the red, I don't think you'll see it happen very often (if at all).
Also, for whatever it's worth for any readers who think the lockup issues I've seen are just my console, I did see some posts on the 2k forums from people who've experienced the franchise crash and others (on multiple forums) who've seen lockups in situations in which I've never encountered them. These problems are real and they're in the game, folks, and the patch hasn't addressed them (at least, not all of them). If you play franchise, I encourage you to keep multiple saves that aren't from the same point in time. (In other words, play a couple games, save your franchise. Play another game and save to a new slot, while leaving the old one as it is. Don't keep your multiple franchise saves at the same exact point in time.)