Talking about the rune counter I agree it would have been nice to have as a UI element in regular play, though we did have the total room amount and how many you had within the pause menu screen, it wasn't very intuitive to find. That's the only way I could make sure I found them all when I was doing my last playthrough of it. I also didn't use a mouse, just the arrow keys. I wonder how much that affects the difficulty of making precise jumps.
We had planned on different upgrades too and showing them as UI elements as well, but didn't have enough time to implement. We also had some more levels and mechanics like spinning lasers (also fire, electricity, and irradiated water, and of course more enemy types) that we didn't get to add, and that could have been something that turned on if we wanted to keep the backtracking. I do really like the idea of the hallways crumbling and maybe having a more open layout for levels and the map in general so that traveling around isn't so unidirectional if we ever revisit this game again. Something more along the lines of Rainworld maybe.
Side note, we didn't really optimize for mobile, but it is possible to play on it. The only problem is that you don't have regular movement, only the jumps, but I do think it'd be a really interesting challenge to try and beat the game in a Broken Legs Run or something. Definitely Rage inducing. It's hard just getting the first pulse lol.