Using the level design is a pretty clean choice, yeah. UI can be useful but it has its own problems like you mentioned (and to make it feel 'in character'). 

I'm curious how the camera would have moved - like third-person-shooter style, where your aim becomes closer to the player character perspective? That would be a huge change, but it could also look good - I'm not sure how else the camera would move around after having played the top-down version. TPS-style would probably by itself make identifying where to go next a lot easier even without having to change the level design, if that's what you're talking about, since you could just look around for any remaining objectives in a room at that point. That's a pretty big shift from where things are currently so I'm not sure if that's what you mean.

Also, on the levels - not so much the level design, but the environmental art lol: I did notice you did have actual rooms with creatures in them, which stuck out as a good detail for establishing 'this is a lab', alongside the tubes along the walls. Maybe having some more of the immersion-tubes in some arrays on the floor might help provide some visual anchoring? I liked the rooms though, their inclusion made a big difference in the atmosphere, to me. If you kept developing this, I imagine some interactivity with the rooms would open up a lot of opportunities.

In my initial comment, I said that the colored circles were more helpful than the stacked cards for indicating which finishers/damage types to use - this was sort of true and sort of not true. The useful part of the circles is that it was easy to if multiple enemies had the same damage condition; the useful part of the cards was seeing what damage condition came next, to quickly chain them together. That's part of what actually made this game fun for me was successfully chaining damage types, and especially if I could do it to multiple enemies. If there were a way of unifying those displays, like... a circle with a prominent (current) damage type vulnerability on top, and a secondary vulnerability on bottom (more than 2 might quickly become visually overwhelming?), it might give the player the best of both worlds? But any way to encourage the player to be able to read any potentially good sequences effectively - it might open the door to stuff like "there are 2 mobs with damage type A then C, 2 with type B then C, and 4 with type C; if I quickly hit A and B, I can then wipe out all 7 with C" which would feel good. The mechanic regardless of implementation is kind of like cycling antibiotics. Or... bejewled? I wonder how a wildcard damage type would do, on either a lengthy cooldown or use-once item or something. That kind of thing would probably make more sense the longer your game got.

Sorry this got long. To wrap it up, I think this was a total success especially for a solo developer. I agree audio would be great, maybe next time you'll be able to get some in without having to sacrifice too much somewhere else. It can be hard to get "right enough" so it's useful or cool, but also not annoying, especially for stuff that happens constantly like the primary fire. That in particular would have taken some time to get right. Not right can definitely be worse than silent. As it stands I think you got a ton accomplished. TWO bosses! Nice job again, and thanks for reading (sorry; brevity is a muscle)