Based on what I've seen, Fire Emblem's linear missions and wide variety of characters are generally better for story, but the more open and lenient nature of the FFT series makes it funner to play. I personally like making Ninja/Paladin hybrids. If I tried shenanigans like that in Fire Emblem, I'd be punished severely. Of course, I've only played these games on the GBA, so I could have the wrong idea.
Love and tolerate.