They both share in broad strokes the narrative set in a medieval political drama and the turn based combat but the games are very different
As any Matsuno game, story and atmosphere come first. And he does a damn good job at that, you'll be engrossed throughout with the way the whole drama unfolds, because it really pushes the boundaries of usual video game stories. It'll stay with you.
Combat system, as any Matsuno game is gonna be a little more needlesslly complicated that I'd want, but not polish enough to go along with it. It's a great game but it does have issues.
Fire emblem story isn't as good nor does it want to. The snes games are better in this department though. However, in terms of gameplay, this series reigns supreme in the genre. It's beauty lies in it's simplicity, and you'll probably end up loving it.
What to play right now? I'd say if you want to make a long investment go fire emblem, if you want an even longer investment go FFT, but you can't go wrong with either