Like any other power system (in the original sense, not the 4e sense), whether or not it belongs depends on the setting. Some settings shouldn't have priests working miracles (spells, whatever), some don't have arcane type magic of any sort, some have powers of the mind and inner strength, etc.
The 'fantasy' genre also has a strong history of it, and still does. Brust's Taltos series has at least six different types of magic (psionics/witchcraft, orb magic, old magic, chaos magic, divine pacts, and dwarven crafting. Darkover more or less a fantasy setting and is all psionics. For a recent example, Webber's War God series has three types of magic at work (magi, wizards, and champions).
So I voted yes. It needs to have a, reason's not the right word, but it should have a place in a world, just like wizards and clerics should before they exist. A good rule system should allow for magic other then the traditional D&D wizard (Vancian or otherwise).