dtgreene: They don't have to be secondary to standard leveling; they can *replace* standard leveling, in that they can be present in games that don't have standard leveling at all.
I'd say that good RPG must have good interesting and captivating character progress. And as such, it is great when it combines different subsystems.
For example from my favorite games, Agarest games - they provide you with standard leveling, crafting, leveling gear, enhancing it with gems, going for various titles (which in later Idea Factory games provided permanent stat buffs), etc.
Labyrinth of Touhou II - it has standard leveling, stat leveling, skill leveling, crafting, stat imbuers and tiered class system.
Disgaea (though I actually dislike it for some moments) - it has standard leveling, reincarnations, leveling skills, upgrading classes, upgrading equipment which had dozens of tiers, 4 major subtiers, and then you could modify it by messing with Item World.
I started getting turned away by modern Western RPGs entirely due to extremely shallow character progression. Low level caps, level scaling, no respawn, roguelike, bweh. It seems that Might and Magic games were the finish for Western RPGs.
Btw, speaking about Might and Magic VI (and VII; to lesser degree about VIII and IX), it has standard leveling, skill leveling, equipment, permanent buffs from various fountains, barrels, shrines, black bottles, cauldrons, etc. Skill leveling consists of 3 tiers. There is also class promotion, which you do twice, and it empowers your characters significantly.
I liked how skill system was made in EverQuest I and II (though I am not fan of MMOs for many reasons, but played a bit some of them): you level your skills by using them, but each skill has cap. The higher is your character level, the higher is the skill cap. I wish The Elder Scrolls games had similar skill systems instead of the mess they had (and minus the level scaling).