When you are talking about the 3rd overall pick, I think you go best available player. Whatever you have in your system right now, this player SHOULD be better (well, since we have had the 1st pick a few years ago, that is a conflict with that statement). These are the guys you hope will take you to the promised land, these are the future stars of the game (you hope). You don't look for a position just because it is not as strong as others, you do that later, with the very top picks you look for that player that leads your team.
Honestly, we are more loaded with (supposedly top pick) players in the OF. While we have middle infielders, anyone we get with this pick should be better than all of them in the long run.