I like the fatigue system. Mana is really a sort of "mental fatigue", but rather than having two types of fatigue it is better to have just one.
I prefer the fatigue system because it makes fighter/mage hybrids more balanced since they do not have two pools to draw from. Everyone has the same pool. I also saves having a wasted stat for non-magic users.
There is a PnP RPG system called "Ars Magicka" which has the best magic system I have seen. It uses fatigue.
Another PnP system I played, called "Pendragon", used a magic system where the mage ages a certain amount for each spell cast. The aging is initially temporary and will be eliminated by sleep within the next 24 hours. The amount of sleep depends on the amount of aging, with mages sometimes having to sleep for several days (magical sleep) to recover. Mages also have a spell capacity, which was a sort of limit on how much temporary aging you could gain in one spell. If the mage cast a really powerful spell she could exceed the spell capacity and the excess becomes permanent aging. Mages could increase their spell capacity by holding magic foci (e.g. a wizards staff) or by casting the spell while in a special, magical, location (e.g. a stone circle, a pentagram, etc. - it depended on the type of spell).
The more fatigue you have the harder it should be to get rid of. The rate that you recover from fatigue is non-linear. Cast a small spell and you recover the fatigue instantly. Cast a large spell and you may have to sleep for a while to recover.
Personally, I would use a magic system that is a combo of the systems from Ars Magicka and Pendragon. A mage would regain from fatigue quickly unless he overextended himself by casting powerful spells or too many spells in too short a time. The fatigue gained from casting a spell would be variable, making it harder to predict the effect on fatigue. If a mage exceeded his maximum fatigue then not only would he collapse, he would also age. This allows the mage to cast that powerful, party-saving spell even while very tired, as long as he doesn't mind being a year older when he wakes up.
I also like the idea of mages have a chance to cast each spell successfully, like in Morrowind. I think it is pretty unrealistic when mages always cast their spells, especially when missile spells have no chance to miss their targets. Compared to a melee fighter or archer, who have to roll to hit, that seems unfair. I would make the chance of actually not casting the spell fairly low but the amount of fatigue the spell causes would be tied to the casting roll. In other words, get a good roll and you will incur much less fatigue than from a bad roll. The roll could also determine how powerful the spell effect is (e.g. duration, damage). Mages would be able to train in casting different types of spells, which would mean higher rolls, better effects and less fatigue.
