Mmm, well, I'll agree that FE and FF are really great series of games, but the two don't have really similar qualities, but, of course, I'm a biiig Fire Emblem fan, so, of course I have to go with that, ahah. But don't get me wrong, I honestly love some of the Final Fantasy games, like FF5 and FF3.
My only peeve with them is I can never really relate to Final Fantasy characters much - sometimes I feel that some characters in those games are.. kind of shallow. Well, Fire Emblem has a lot of characters like that, but, honestly I think Final Fantasy could of had the potential to stick out more. Another thing is mechanics; I find the mechanics in Fire Emblem more easy to get than Final Fantasy. Of course, Final Fantasy does have really good and interesting mechanics, but, I feel as though I can be more -technical- with Fire Emblem. If that makes sense.
But again, both are great series of games, and I can't wait for their next installments.