Personally what I really dislike more than "one thousand classes" is the multiclass system where you can make your "piece meal" build taking one level here and one level there, etc. As if making a character was some weird buffet. It's something I don't really like in principle even in D&D and Pathfinder just makes it worse.
I do find that kind of multiclassing incredibly intimidating. I was never able to grasp full benefits of each level up to successfully plan out my builds - be it DND 3.5, or Pathfinder.
