You know adam, I had already been thinking exactly that after reading the feedback so far. I was trying to think what would be the best way to address the 'blank' sections, and I think you're perfectly right- make the contrast more defined, almost black them out. TBH, it was HFA that inspired me to set out and start pixeling away, and I had been poring over tons of old pictures of SNES games, particularly Super Metroid.
I think I'll increase the variety on my doodads (and fix those crystals), maybe clean up some of the backdrops and add both some particle effects in the background layer with the aforementioned space debris, and definitely pump up the contrast on the floors. I'd be trying to avoid some cliches of the pixel art, and not end up with a game that looked like Limbo or Braid after shaders, but I think darker terrain is just what the doctor ordered
Now I haven't had time to clean this up yet, but do you think this is a step in the right direction at least?
I need to lighten it a little and smooth the borders, but it might be the right way
If the purple stuff is alien 'grass', I hate to think what that asteroid is. Yeah I'll change that one
Its hard for me to work in the purple to this "Red & Purple" theme, I'm going to play around with some doodads and maybe tone the fog effect a shade of purple
I would suggest making the grass more of a red/brown tone, in keeping with the rest of the level whilst ensuring it's still recognisable. I would probably draw some real grass, then change the hue to something closer to the reds in the level.
EDIT: also, i would make some tiles that blend the grass into the rocks more, as well as some that make it look more patchy. At the mo, it looks like it's too "stuck on", like a rug of grass just lay there, rather than being part of the natural vegetation
Try changing the hue and saturation levels on some of your shades, eg. all the shades of red on the ground are the same red hue, and the saturation of the shading is at 100% for each shade. Just my thoughts though.