It may be Metroid with a snail...
But it's a damn good game! Everything from the sound to the level layouts and enemy positioning was stupendous. Metroid is probably one of the hardest NES games to reproduce without copying and you did a wonderful job. The whole wall climb mechanic is extremely well implemented and everything is very, very smooth.
As for improvement...
For the most part the graphics looked great, but i do feel that you could have put a tad bit more effort into the snails themselves. The flowers, walls and enemies all have shading, but the snails seem to void of any lighting whatsoever. This is minor, however.
The only glaring problem I felt this had was the invisible wall's foreground images. If you could have dimmed them a bit or something so that we could see where the snail was after being completely inside a secret area then that would have been much better than wondering around blindly. Also, the bullet layering is a bit weird in them, too. While firing any sort of projectile while inside a secret passage you were able to see the bullets as if they were coming from nowhere. This issue could be solved by making rendering the ammo 1 layer deeper than the walls, so fixing it may or may not be something you'd like to do.
Overall, this is a really fun game and I enjoyed every second of it. Yes, it could use some tweaks and such, but as complex and massive as this I'm not surprised there isn't more. Thanks for making this, it was a nostalgic blast! Grats on the Daily Feature and keep up the great flash games!
~NorthboundFox