The fact that there are 'builds' for characters and one needs to pick feats, etc. in a specified order is IMO, one of 3.X/Pathfinder's biggest failings.
I would like a game where I didn't have to have any idea what my character would be like at high level -- where what that ended up being was more of a result of the story, and what happened to him over time. For that to work, prereqs for feats have to mostly go away, so that you don't have to make choices at low levels that enable others at higher levels.
Ken
I view it as one of its strengths it allows customization. Sure you have to make some choices at early levels as to what you will be able to do at higher levels but it is really not that difficult and it mirrors life in the fact that you are training for those higher feats.
Yes it can be hard for a newbie but once you know the game it is really not hard to say okay I want this fighter to be all about dex so I am going to take these feats. Or my wizard is all about crafting so I am going to take the crafting feats.
With feats and skills of my choosing I have a better chance of making my concept then if I used a game designer's vision of how this theme ought to be. Which is one reason I am not crazy about themes.