Let's see, a couple of things....
Firstly, that bit you mention about enemy count. That I think is something to put onto Mantis to make sure everyone can see it, since that sorta bit is one of those things that will create the "feel" of the overall game. Heck, you could almost put this whole thing on Mantis as a feedback report. It just makes it easier for everyone to see it. I have the time to check the forums alot, but everyone else might not.
I'd say, bring up that bit about the rooms and such as well on there.
As for the enemy count, this specific bit would be a little wonky right now anyway; there's only so many enemies available. In addition, something that might be slowing down the whole experience for you... and thus, changing it up so it "doesnt feel like a shmup" is the fact that the HP on enemies (and bosses) hasnt been balanced AT ALL. Like, it's not been touched. I've just been slapping the same number on many things, but have asked Chris about this, and he's pointed out that with so many items not in the game, and all of those items being hugely responsible for your stats, there's no point in worrying about enemy HP right now. So some things that shouldnt take long to die will take forever, as the usual result seems to be too much HP right now instead of not enough.
Let's see... what else....
Sounds, most of those indeed just arent in yet. You can probably expect the usuall array of explosions and other explosions that you get from Arcen
Mines, you can blow those up with missiles.
Backfire boss spawning on you, I could SWEAR I turned that stupid thing off. I distinctly remember telling it not to spawn right now.
Brick enemy being weird, that enemy wasnt supposed to be spawning in the first place, it's not finished, so it's all glitchy and weird. I hadnt realized it was spawning like that but it should be fixed up when .137 comes out.
Shields simply regenerate whenever you switch rooms.
Bosses being disconnected from their environments: This one, honestly, I think isnt going to change all that much. ALOT of games of this type have this sort of issue, since when the bosses for a stage are chosen randomly, you cant really tailor the level to them very much. Isaac being a good example; Monstro is still Monstro no matter where you encounter him. It doesnt make a whole lot of sense for him to be hopping around inside of a cathedral, but he'll still be there anyway, making a jerk of himself. And so it goes with many games like this, in that enemies and bosses can seem a little disjointed.
As for consumable item effects not doing enough (I agree) that's another thing you should write up onto Mantis; I'll probably add my own comments to it afterwards.
Now outside of that, any specific feedback on the enemies/bosses or whatever? Like, are any of them too annoying, or too stupid, or does any of them seem broken somehow or cheap or anything like that?