I think Yahtzee said it best about turn-based combat in his review of Super Paper Mario, it's about as compelling as using the toolbar in Word.
Largely, turn-based combat is tedious and time-consuming. I can see that slowing down combat to make it into more of a strategy game would be interesting, but most of the time it's poorly executed. And this varies from game to game. Some games have you set up what each character in your party is going to do a few seconds before their turn actually comes up, which can be pretty goddamned annoying if the target you'd selected dies or runs off and you helplessly watch your retarded barbarian swing his Great Axe of Skull Cleaving at empty air.
But, often, there is no strategy involved beyond making everyone hit the dancing goblins as much as possible while having someone heal up or resurrect the others every other turn. In fact, healing magic just plain sucks because all it does is lengthen the process since your party lasts long, so the enemies need to be tougher to provide a challenge. I suppose it would be alright if you had options beyond "I hit him" but you don't, really. It's just Rock'em Sock'em Robots, only much worse.
By process, I do mean fight, and it's a dreary experience. Every time a character gets and action, there's a brief animation while they take that action. The first couple times, it's kind of neat, but before too long, you start wishing you could skip it like expository dialogue. Especial stuff like those Summons of GFs or whatever they're called in Final Fantasy.
So, mostly it's a balance issue, I think. Even minor fights seem to go on for hours and the amount of damage you can take and dish out is just ridiculous. Doing limit breaks where you do 99999 points of damage for twelve hits in a row and the boss still has three quarters of its hit points left, then there's something wrong here.