I am surprised that no one mentioned the Age of Wonders series yet; they are TBS games in the tradition of Master of Magic, just like FE is. The newest game, AoW II Shadow Magic (from 2002!), is still superior to FE is many aspects, most notably user interface, magic, and tactical battles.
I haven't played Fallen Enchantress yet, but I *hope* its magic system is better than AoW II. While a great game in its own right, I feel like AoW has the worst work to payoff ratio out of any MoM based or inspired game barring the original Elemental, including MoM, AoW, Fall From Heaven 2, Warlock, and Dominion 3. You spend incredible amount of time, resources, and manpower to gather mana, research spells, expand your domain, and position troops... all for a handful of uninspired buffs, summons, and attack spells. In MoM you could feed, fund, create, immortalize, mobilize, waylay, cripple, and destroy entire armies, turn the world into a giant lifeless mana battery, and levitate fleets of warship out of the sea. In Dominion 3 you can shroud the world in darkness, summon beings tantamount to gods, and protect your provinces and bolster your work force with an army of illusions. In AoW II...there's one really good high-end attack spell that doesn't rely on inflicting status effects, and those tier four summoned units really come in handy augmenting your army of tier four units that don't require mana.
None of those games have a balanced magic system, but AoW II is balanced in the wrong direction. AoW II's combat system allows you to bring 3 stacks of units onto the field, and often expects or requires you to do so. A well-placed fireball or a tier four summoned unit can do good damage against a single stack. But three stacks? Not so much. AoW II's magic system is a forecful shove to MoM's punch to the face. When magic is a subsitute for a tech tree, I feel dominance in magic should equate to dominance of the world. And I think that's where a lot of fun in the MoM inspired games come from. In one of the GameInformer articles I read about Elemental, it mentioned that magically was purposefully overpowered. While that was entirely untrue of the final product, I'm hoping that holds true for Fallen Enchantress.