These are just my opinions based on what I've seen. There've been a couple great youth ballplayers that inexplicably left the game during college.
Parents that become too involved, and make their kids success too much a part of their life (watch Searching for Bobby Fischer). If your kid really good at something, some of his identity will bleed over onto the parents. This is the primary reason I've never worn team gear - I was always there, at most every game but for him specifically - not as part of the team (that solely belonged to him). I loved and still miss the youth baseball team social circles, I just feel it's good for the kids to understand we're supporting them and we're not a part of the team.
Priorities and balance - I think as some kids become adults they decide that girls and other things are more important now that they have a choice. I think that lack of choices when they are younger and their desire to want to please their parents can create a big shift in priorities when it's totally their call.
Loss of identity, If you've been really good at something you're whole life (everyone has told you so - including your parents) it becomes who and what you are. That kid is really good at baseball, that kid is a ballplayer, that kid is a stud... Then they go to college, and they're average or less than average until they progress (if they progress). I think this one takes out some really good ball players that didn't push through it.