You can have race and class, and flesh out the character with virtues/flaws. CoQ does this to an extent with mutations. But it can also be more general traits. I remember the tabletop roleplaying game Ars Magica having a really good section of virtues and flaws, in addition to stats and professions. I think special traits can give the character some personality, from a "fat, literate fighter" to a "claustophobic, fasttalking mage". DoomRL and Infra Arcana spring to mind as using perks in a cool way.
Depending on the kind of character creation system you want, classes/professions can be more or less vague. You can include "archetypes" with a preset assignment of skill points etc. and let the player assign the last points manually. Eg. you pick a race, which sets some stat limits or whatever, and a class, which starts you out with a basic survival skillset, and then let player choose five traits to raise/gain. Gearhead has a system reminiscent of that, with dozens of professions ("fireman", "arena pilot" …). Incursion has a very in-depth character generation system, but I just barely played it, and many years ago.
The possibilites are endless, I guess
As always,
Minotauros