I always like new storylines gameplay in my favorite games :d. Part of the reason Age of Wonders series is such a great game from my standpoint.
Oh, and I should note that Age of Wonders I and II have some GREAT tactical combat. If I could pull from that as well. . . lets just say I would pull a lot of the base mechanics from it. Such as not using a square grid for battlefields. And having penalties to counter attacks(so one super unit can't pawn an entire super sized army of more than 20 units. . . well at least in II). However, even better would be something similar to Vanguard Bandits countering system. And I certainly wouldn't bring out Wonders's move all units at once deal(I like speed counters/weight times!)
Of course by that point it likely wouldn't be recognizable as a Final Fantasy Tactics game anymore. Or is the 'setting' of final fantasy enough to pull that off?