Another is the Anarchy Online system, which I am a MASSIVE fan of. I"ve never pushed it hard because I"m not sure how much of it is my personal taste and how much it really is a superb system. In my opinion, it is as innovative and has as much and more lasting benefit than FFXIs job system (withoutsub jobs).
For those unfamiliar with it, the game has "Mission terminals" in the cities and hubs (you can get an idea of it from . You set a series of sliders with a range of mission parameters and it generates a list of instanced missions with an objective from a pool (eg assassinate a named NPC, retrieve an item) and a specified item reward, which can be a piece of armour, a weapon or a skill.
The missions scale according to the number of people in the party and their levels, so its good for anything from 1-6 party members. This system has been easily catered for in expansion after expansion, with increasing level caps, in AO.
If you combined this with the ability to raise all classes on your main character, the longevity and replayability of the two systems would increase exponentially. I can"t stress just how much I love this mission system. It perfectly combines the pure MMO experience, with the D2 experience, that Caliane is discussing above.