Nerf levels and nerf XP. With a "level" system, you create the illusion of a beginning and an end in something that isn't supposed to have either. Characters start at level 1 and are finished (in terms of advancement) at level 200. A friend of mine once said to me "You never stop learning until 15 minutes after you're dead". When I reach level 200, my character dies as I cannot learn anything more. Upping the level cap will only make that process appear more drawn out than it already is.
Let whatever used to give XP give IP instead and let mission tokens be worth 1 IPR point per physical token.
Remove the skill / breed caps and let people put IP where they want to when they want to. You want to talk cookie-cutter...this skill system is very cookie-cutter. If it were a system where a character could spend points in whatever skills they like whenever they like, the specialization possibilities are endless. As it stands, everyone has set of caps that they hit and thus everyone has the same general abiliities.
Remove all of the level requirements on ANYTHING that has one and lets go back to a skill-based game.
Let the profession choice determine the nanos in your library and the cost of improving skills.
Let the breed choice determine the cost of improving your base abilities.
Got coffee?