generalripper: End classes outright. Classes are the worst thing that ever happened to RPGs.
RPG's suffer from classes, but people suffer from choice so we're stuck with them. Some people are indecisive, some are stuck in a box and the ability to come up with something outside of that box is incomprehensible, some can't do anything unless they have a fallback excuse, and some are just lazy. The idea of forging ahead and creating your own unique character is anathema to most of the population, and if you've ever gotten drunk before asking a pretty lass out , starting a fight, or making a major decision, then you're officially normal and part of the problem. :P
Unique because any system based entirely on skill points would end up being relatively unique to each player as each person would choose different skills unless some were obviously better than others. If it's something like Deus Ex Human Revolution where non-violence is more powerful than a violent approach then a general tendency towards non-violent specialistion is to be expected, but otherwise a more chaotic effect without any major trends would be the norm.
However, Fighter, Mage, Thief, has everything there you need to make anything else. Thief has the skill points to go the diplomatic/sneak route, Fighter the tankiness to slog it out mano-a-mano, Mage the ability to tell the laws of physics to take a hike. Anything else in the normal RPG is simply a combination or variation rule. In most games you aren't limited to a single class, so you can go Fighter + Mage = Bladesinger (That was in NWN, yea?) or Thief + Mage = Assassin/Bard or Fighter + Thief = Pirate/Corsair, etc.
Even in your sci-fi/realism RPG you'll still have the Brute, Smart, Skill archetypes. Smart will be the engineer/hacker, Brute the basher, Skill the sneak/diplomat. Which would be the reason they're so popular. :P Simple enough for a computer, easy enough for reasonably unlimited variation.