I've had three problems with the game so far.
1. Really wish there was a way to speed up enemy turns. There are times, especially during the extra-ops, where you spend like 60% of the time just watching 'Shuffle Shuffle' pop up around the map.
2. A really easy way to break the game is to pick up the SMG from the... second non-tutorial mission, I think it is? You have to kill Ty the Immortal for it. He's hidden in the grass to the right of where the not-city team starts. Equip that onto Rosie (The lead Shocktrooper) and send her into the Scout Mastery challenge n' just run around the map gunning down the Elite Scouts (Save before taking on Oswald the Gold in the event he evades your gunfire and one shots you). You get a TON of XP and cash from doing that easy mission as well as Oswald's ridiculously accurate and powerful rifle. It basically turns any Scout into a long range Shocktrooper and can destroy light tanks in three shots.
From what I can tell, the 'mastery' exercises are meant for mid-late game and balanced as such. But they don't actually limit what class you can take. Scouts are supposed to be terrible for direct combat and the Imperial Elite Scouts do tons of damage. But if you send a properly equipped Shocktrooper instead... they can make easy work of the Elite Scouts where one of your Scouts would die almost instantly. I've attempted all exercises but the tank one, and it seems like the Scout challenge is the only one that you can really cheese in this manner. I almost completed the Sniper challenge using a Scout equipped with Oswald's rifle, but... meh. Maybe if I sent two they could get the job done. Shocktrooper in particular seems pretty bullshit, considering that Rosie starts out facing at least four heavy Shockstroopers with zero cover and no support. She died before I could even enter targeting mode.
3. In order to get A-ranks, it seems like you're supposed to just rush 2-3 units past the enemy forces to backdoor the objective. Like... completely circumventing the gameplay in most cases. Just kind of seems lame. Example: In the first skirmish, you can attack the enemy fortifications head on and fight through the small army stationed there... or you can just run around the hill and only encounter two soldiers, then kill the one guarding the base to finish the mission for an easy 1 turn A-rank.
I think the game is great and I enjoy playing it, these are just some grievances I have.