Hey, glad you like the game and thanks for the extensive comment. :)
Controller issue:
I have pretty much only tested it on two different controllers and both are knockoff playstation ones, pretty sure they don't have this disconnect problem though, assuming you mean unplugging and plugging in while the game is running, so not really sure what to do about that at this moment.
Diagonal fire:
This is something that would definitely improve the game so I've added backpedal aiming to the to-do list, so I'll be trying to add that at some point.
Story:
I have a general story line planned out, but I haven't decided how it's going to turn out yet as I have multiple versions of it laying around. So I'll be combining / choosing among them to make the final story line when the time comes. I know this doesn't exactly answer your question but that's all I got to say about that for now.
Diverging from metroid:
Well, this is always going to primarily be a VERY metroid like game so that is always going to be there. My general idea about the game is something like this - metroid but not metroid at the same time. So if everything goes as planned, I have a lot of non metroid things coming to the game. Not sure what else to comment about this so you'll just have to wait and see.
Other elements:
Well, this can be interpreted as many different things so I'll just say, yes, there will be many different elements added in the full game.
Progression:
Yeah, I have big changes planned for the beginning of the game in terms of progression. Like finding parts of the suit instead of just helmet then straight to full suit, which I'm guessing is what you've already read about. And that is definitely how I want the game to feel - building up from nothing.
Teases of lore etc:
If all goes as planned, then there is a reason for the bodies to be there, let's just stop there. ;)
The bot is going to stay, but I've changed it a bit so it goes offline at the in the first save room as I feel it didn't really do anything after that. It was pretty much always supposed to be a tutorial only thing anyway.
So, I hope that answers some of your questions, thanks again for the extensive feedback. :)