Its really Fun. I like the Concept of Rougelike Fire-emblem-like, it fits well together, you aren't as mortified when your Units die, as you're getting new ones constantly, I like that the Enemies aren't just nameless Goons, but have randomized Names, gives them a lot more Personality.
It could use more Variety in Events, and some (generated) Leadup to a mission, a small Briefing or intermission of generated Information why you're there, what brings the Enemies to it, etc.
Portraits and Unitsprites clash, in Pixelsize and in looks. Consider keeping the Portraits greyscale aswell, so you can change their Uniform Color depending on Team. Then add some Heads to swap on your Unit Sprites to more closely match the Portraits, to give them more Personality. Doesn't need to be a perfect match, that'd be stupid, but if the generated Portrait has long hair, give the Unit long hair aswell, if it has a Hat, give the Unit a Hat, and so on.
Also some Dialogue on recruiting a new Unit would be nice, generate them some personality Traits, and based on that a bit of Text, just a few Lines.
That's generally the big Point I have I guess, it needs a bit more Story to it, you could generate that very easily aswell, its just Text. And the UI needs an Overhaul, the Grey around the Playable Map looks bad, but that Stuff is obviously a Placeholder at the Moment.
I didn't play a lot of Missions, but from what I've seen, the Maps are fairly decent, but could be better I guess. You're making some nice Chokepoints and alternate Paths, but scatter Buildings pretty badly.
(Also, if its more Rogue-like-y, consider generating your Maps, even if you randomize Stats and Portraits, you only have so many Unittypes in the End, with a non-ridiculously sized Weapon Triangle, so replaying the same Missions all the Time could get boring quickly. If this has a decently well Map generation tagged onto it, with good intermission between the individual Missions, bigger Battles later on, a Camp to manage your Units in between or something, this could be a very nice Mercenary-Management Game or something like that, where you'd be able to repeatedly just come back to and play one or two Missions if you're feeling like playing a FE-Tactics like, getting a mostly fresh Experience every Time.)
You could also overtime bloat this with a lot of interesting Encounters, wild Animals, mythical Beasts, different Landscapes, Weather Conditions, and whatnot. Theres quite a bit of Potential here I think.