You really have a solid base here. And the fact that you want it to take to perfection is great. So, here's my input. As always, I'm not expert, and this is just my perception.
One thing I noted is that the walls have a lot of details, but the furniture and the character are a lot stylistic in the details. This inconsistency make the rooms look unfinished. Adding more details to the sprite, and more furniture to the rooms can help with that. Or try to make the tiles of the wall less detailed.
For less detailed brick walls try taking reference in cartoon. Nothing is more styled-from-real-life than cartoons.
For example:
Look like not all the walls are not completely detailed. Few bricks here and there, plus the right color, can give a lot of information without saturating the room visually.
Also, you can take the old edge approach for tiling. Only rendering details on the edge of the iluminated tiles can do a lot of things at once:
Saving a bit of information/size on the tileset.
Focusing the attention on the action and usable parts pf the map.
Reducing the visual noise.
A good example of this kind of tileset for 2D games is the really fun game Monster Sanctuary:
See how everything is so detailed on the map, yet the attention and focus of the visual is always centered on the important parts. Every (usable) surface is detailed, but the entire scene doesn't feel cramped.
If you go for a more detailed feel room, that's equally cool. Your current wall tiles are very well done. I'd recommend using more real life reference to fill the room with life and make the scene less empty. Emptiness when not used correctly in level design can make things look boring or incomplete.
For a good examples on how to overly fill a room and make look awesome you can check Owlboy or Scott Prilgrim vs the World:
And finally, some toughs on specifics of your levels:
Water Path:
Really like the idea of the wooden path. Looks like a door to me. The background wall needs more information, just looking at the scene I don't know if it's a port of a sewer, under or above ground. Some details giving context would be great.
Laboratory Interior:
Really digging the lasers here. But labs need more tech stuff! Some wall computers, surveillance cameras and weird tech around would help a lot this lab. Also, the background, try not to use patterns so embroiled. Think in what kind of walls a lab would have. Plain old white-ish, with a few guide lines would work (think in a hospital for example)
PSI Building Interior:
Be careful with colors! The legs of those tables look like place-holders, because of the color decision there. I would highly recommend to pick a color palette and stick to it.
For more information on colors palettes I recommend:
https://lospec.com/palette-listHope this help you! And keep it coming, you are doing awesome stuff here.