Hey there, thanks for the feedback! I'll do as I usually do and give a few specific responses here...
For Terminus itself, what you ran into is the game's biggest issue right now: Balance issues are causing the difficulty progression to be effectively backwards! Ignoring it's two guardians, Terminus itself has about 8400 HP... that's a pretty big amount in this game. And each of it's guardians has about 3500-4000 on it's own. That's a lot to chew through. But player power/damage progression is all sorts of messed up right now, so that often, by the time you get to him, you're WAY too powerful for what you're supposed to be at that point in the game.
It's not just that boss, people have had it start to happen as early as floor 3/4, so they end up flattening those bosses and the Warden as well (and the Warden has a bit over 10000 HP...).
That's been one of the biggest concerns, that whole issue, and we've got an upcoming patch that'll finally fix that; I've been testing it a lot recently and I have to say, it works soooooo much better now. PTarth, one of the Freaking Volunteers working on this, did all sorts of crazy math stuff and did awesome huge changes. I assume there were arcane rituals or something involved.
Other than that, I've been fixing up tons of the game's broken rooms (it has many), so the balance change, and the room fixes, are coming in a big patch probably before the end of the month here. We still need to test more, but I personally think it's looking really good. And then there's other stuff being worked on behind the scenes that I'll not speak of for now.
Now, as to some of your other points:
Time Warp: Yeah, I know, damn thing is everywhere. I've set it so that it actually only appears in the secret room, much like the item from Isaac that it mimics. It's powerful as heck, it shouldn't be appearing every blasted time...
Energy Shield: I forget what this does. I think, in our development version, this may have already gotten changed though. I *think*. I could be wrong. One of the others can throw a virtual chair at me if I've gotten that wrong.
3 win requirement: That bit is staying, I think.
Floor challenges: You know, I kinda agree with you on these. I like the idea of these in concept... but I don't feel they were really executed right. But, not sure what to DO about them. Something is likely to get altered there, but I've no idea what. Even just something like "Don't use missiles this floor" is often not worth it, because by not using missiles, you're probably missing out on health shards, money, items, secret rooms... the benefits of using them far outweighs the rewards for not. Among other issues.
Middle shop item: Wait, what? I... what? I've never seen this. Is the default key binding for "grab things" also defaulting to an attack key? That shouldn't be the case. Or am I reading this wrong?
Sacrifice shops empty: Actually this is what happens when it's item pool runs out, heh. I'm going to stick some more things in there, get some variety in that room.
Story text: Yes, this is missing, isn't it... call it a casualty of development deadlines. We're going to get more story stuff in there. I'm not sure WHEN, but it'll happen.
For your suggestions...
Boss rush: Yes, I want to see that too. One thing though, if you want to just test your skill against a particular boss, EVERY boss room can be found in that "mods" button in the bottom right of the screen. There's tons of different rooms used for testing in there, and that includes a room for each individual boss; you can pick one, select your difficulty, and in you go. You'll start with the White Gloss mech, and 5 missiles. If you want to see what a boss like Terminus does when you ARENT all-powerful.... that's a good way to see it, heh.
More sacrifice shop items: Yep, that's coming! We've got a pile of item pool changes coming, some of that is going to come along with the big balance change.
More early bosses: Oh yes, I can do this one.
More music: Out of our hands, sadly.
Difficulty connected steam achievements: Ah, this one is a good idea, I'm kinda surprised it isn't already like that. Even if they are added though, I *can* say that achievements for Misery difficulty will never exist (because I wont let them...). That difficulty isn't actually ready to go yet... what's there right now is a placeholder... but it's going to be hard enough that most players likely will die on the first floor. Next to nobody will actually beat the game on that mode. That mode will go just a bit overboard with challenge so I'm not going to force players that like to 100% games to go through that nightmare to get all the achievements. But for Hard mode and below? Sounds like a good idea to me.
Periphery achievement bug: UGH. I swear, it's always something. At least it's not the Warden again, I'm tired of fixing that guy. I'll let one of the others know about this specific bug though.
Anyway, so that's that!
Good luck with Hard mode, by the way, heh. Just so you know: Hard mode is the one that's hit really heavily by the broken rooms right now. If you play Hard and the difficulty seems to just go absolutely bonkers, well... that's why. Broken rooms aren't so bad on Normal. But they're game-wrecking on Hard. But I've fixed TONS of them and that fix will come along with that big patch.