I quite like job and classes systems, they grant a great deal of freedom to a player, or at least as much freedom as an RPG provides. In most RPGs, characters have unofficial classes of their own anyway, determined by the moves they learn and stat growth, so it's not an uncommon thing, but as I say, being able to choose who is good at what is always nice; it lets you develop your own play style.
But, at the same time, if a game is too heavily dependant on it's job system - for example, Dragon Quest games, FF3, and even the later Disgaea games to a degree - it feels a lot of the time like the game doesn't really have a core set of characters, because you can just substitute them for your own, and they'll do a better job of it. It's at the point when customization becomes traded for character development that I start to go off a job system; I like having freedom to choose and experiment, but at the same time I want a developed party who I can actually empathise with.
These systems are often pathetically limited, as well. Maybe five or six different classes - Dragon Age: Origins, for it's brilliance, was horrendously limited, whereas something like FFV had a huge number of jobs, and the ability to switch between them was wonderful. But RTS games, like FF Tactics, Tactics Ogre and Disgaea: Hour of Darkness, have the best job class systems in my opinion, because the gameplay revolves around them, so there are plenty of options to choose from.