Yeah, it's not 'huge flaws,' it's 'one design decision I don't like.'
Yes, the upgrade fights are frequently too hard. Yes, it would be nice to get an indication of approximately what level you need to be to win the fight. But that's it. One small issue, not 'huge flaws.'
Sorry if I'm starting to sound like a King's Bounty fanboy, it's just that this game rocks so hard I'm often left speechless playing it.
For mine, I have ONE thing that annoys me that I would like to see in a patch or expansion. I would like a screen that gives me the inventory of the various shops. This would be nice as I could see where I need to go to get a particular troop. It could work in the same way as the search for hulls/equipment in Space Rangers 2.