I haven't read all this but I don't see why you need to use higher resolution to add "detail".
+1 to keep cleanly scaled 16x tiles and continue your progress instead of stopping and changing everything to 32px.
Drawing at 32px also takes exponentially longer.
What I think you need most is some design, and here's some suggestions on how to proceed.
I like the dark areas but think you should break them up so they have more effect.
Scatter small "safe zones" (save/checkpoint?) around the place with brighter lighting, perhaps a consistent colour and background to make them instantly recognizable.
In a slightly different setting you might open a door to a small outside area with some environmental lighting (downlights etc) and different ambient sound (weird alien jungle??), then straight back into different ominously dark area.
What would help is to roughly block out ideas for areas in a larger document or on paper.
Rather than getting caught up in detail or obsessing on how they join together at this point, its more about what each area is.
E.g. Horticultural Area with plants and stuff, Reseach Labs, Warehouse, Water Control Room, underground cave area etc.
Once you have a few ideas for areas, you can start to design backgrounds and area transitions.
Even just recycling existing artwork and adding a few details here and there can really do the trick (e.g. the vines have grown over the walls in Horticultural area).
Up to and including this point I'd advise you to start loose, rough things in, don't bogged down in detail that you could potentially trash and regret wasting time on.
These designs can naturally lead into script, puzzles and enemy designs.
And ultimately you could have an explorable map that defines the overall design of the ship/station you can use in the background of the title screen.
Small cutscenes can be gun(not generally a fan of long and boring ones), not forgeting the power of your dynamic lighting.
Sure its been done plenty of times but lests say your briefly trapped in a small room, and the unreachable (for now) corridor below you has a flickering light in which you see a large black beast run through causing a screen shake, after which you're allowed to continue your search for some fresh pants.
If your posting progress following some kind of plan like this you'll get loads of really great input from this forum.
Post your sketches, show us your prerenders and in-game renders etc. Its all relevant.
