It's looking more and more beautiful, it starts to bring tears to my eyes with its flashback-ness.
However I have bad news for you. Devastating, sad news. You will probably have to rework some surfaces.
This ties is with 'omg what's so difficult about Flashback art anyway?'. Well what's difficult about Flashback is that it's very deliberate. There is artistic direction and it is consistent. Delphine had thought things out very very much. Let's look at a flashback screenshot.
http://www.mobygames.com/game/jaguar/flashback-the-quest-for-identity/screenshots/gameShotId,27493/This is from the jungle level. This whole level is lit in this way: the front surfaces of everything are lighter and then the 90 degree walls that Conrad looks at are darker. Not only the vines and shit, look at the door mechanism. Straight ahead, lighter, side, darker. This is how they wanted this level to look and they're consistent about it. Also my theory is this: this level was the first they did early in their development process and besides being amazingly well-pixelled, it's also a little different from all other levels of the full game. Let's look at a screenshot from one of the levels that looks more like yours:
http://www.mobygames.com/game/snes/flashback-the-quest-for-identity/screenshots/gameShotId,117907/and perhaps
http://www.mobygames.com/game/dos/flashback-the-quest-for-identity/screenshots/gameShotId,2986/ and
http://www.mobygames.com/game/dos/flashback-the-quest-for-identity/screenshots/gameShotId,322652/Here we see the reverse. All front sides are pure black or very darker and the sides that Conrad sees directly are brighter. There are various practical advantages to this method, a big one is that the developers didn't have to make tiled 'brick' or similar walls to put in the black spots and there's also visibility concerns, generally it's a better idea than frontbright in my opinion.
Either way you go, you have to be consistent. Right now you have the black fronts on your platforms,
but on your door mechanisms and the like the lights are reversed!. This breaks persepctive and makes the mechanisms look as if they're 'floating' in front of the game plane!
So my suggestion is to reverse the lights on the mechanisms. I know it's a lot of repixelling and I'm sorry I didn't spot it earlier
But trust me, once everything is rational-correct, your image will look much, much better.
Also here's a total color revamp to study.
also main character relaxation pose. Flashback has such a stick-up-ass main pose because of rotoscoping more than anything, they needed all the animations to revert to a standard idle frame that the actor could resume clearly every time. Since you're not rotoscoping... keep
this in mind.