Endgame suffers from poor unit balance.
The game captured my attention and kept me up all night trying to complete it. I don't think that's going to happen now, because a few small mistakes managed to screw me too badly to finish the endgame.
It's readily apparent to me, in retrospect, that elite units are actually far better than anything the more advanced, non-upgradable units have to offer. The problem is that this only became apparent to me after trading in my elite army just to get a look at these incredibly overspecialized later units. Other reviewers have said you ought to have an option to keep certain units as reserves instead of deleting them outright to make room for new ones, and that's definitely an option that would have saved this for me. As it stands, I think the game is unbeatable now. I took too many losses on the swamp dragon, and with the current state of my army they just aren't equipped to get back the gems they would need in order to rebuild a force strong enough to continue competing. Some way to return to easier missions in a situation like mine would also be appreciated.
Also, most bosses could have been handled better. In Patapon, their routines seemed fixed to the same rhythm the player was keeping so that you'd have a fair window of opportunity to react to their attacks with appropriate commands. Very often, your bosses go into aggressive mode when I'm in the middle of a command and can't drop it without breaking my chain and delaying myself several beats anyway. Just as often, they come out of aggressive mode before I've had any time to possibly finish a retreat or defend order.
Your art and concept are good but they just don't carry the gameplay. There are a lot of major flaws here beneath a polished presentation.