the menu overlapping the lowest character will be fixed, because the lancer characterset is temporary, and I'll just make the new one to be a few pixels above.
about making the command window the same height that the battlestatus window, I'm not sure, It doesn't really bother me, and I would have to edit the default command window (or make a new one just for the battle, I could do that, but then there would be even more empty space...
about the battlesystem:
it works somewhat like chrono cross, you start every battle with 0 AP, when you select attack, you can select fast attack, strong attack and fierce attack (fast attack doesn't need any AP to be executed, and recovers 1 ap, strong attack needs 1 ap to be executed and recovers 3 ap, and fierce attack needs 2 ap to be executed, and recovers 6 ap)
so you have to start with weak attacks, and then you can start to use stronger attacks.
when you have enough ap, you can start using skills, those need ap to be done too, but don't recover any ap unlike the attacks. this way you can't just spam powerful skills (at least at the beggining of the game.
Love the detail..but seriously try a version without canopy..see what happens