Random constructive criticism as I played through it:
A new plot rarely works well in a SM hack without a lot of ASM.
I like the rapidfire.
Colors on the suit are a bit disturbing on the eyes.
Lots of tiling errors in the first room alone (may be just the fact that you're not finished) and lots more throughout
Yay its a fullhack (well...sort of).
Scrolling errors in what used to be the old MB room and a few other rooms as people mentioned.
The overlaying BG in the room with the second missile pack looks awkward. It's probably that its hard to see what it looks like in SMILE so its difficult to fix.
Slope problems as other people mentioned.
Whats with the reservetank background room? Woo and then it turns to bombs after you get them
BG in some of the lower Craterian rooms is messed up; you need to change the BG pointer for them.
Torizo is rather boring considering he can't hurt you if you stand next to the door and he takes way too many hits even accounting for all 15 missiles.
Are you sure you want the boss statue that leads to Tourian in the same place it is in the reg SM? (Makes it kind of obvious where it is now.)
I'd say the big problem is the tiling but its normal to have bad tiling when you begin making a hack, you need to get used to the way the tiles work together to look correct and basically only time and practice helps this.
This can help you a bit:
http://www.freewebs.com/blacktelomeres/smilefaq.htmIf you haven't already seen it anyway.