Okay, so I played this, and some parts impressed me and others really felt lacking.
Metal Harbor was pretty garish. You need at least two distinct shades of gray to prevent this level from becoming monotonous. The battleship needs its own textures and refined structures (a satellite dish or radar antennae would do). Scrap the ending and replace it with a huge girder / giant missile set piece similar to the one found in the original Metal Harbor.
If you can’t do anything interesting with Route 101, scrap it.
Final Rush was the most exciting stage in SA2, but was the most boring stage in your mod. The level is completely flat and the repeated *rail* pieces come across as hackneyed and repetitive. Ditch them entirely. SA2’s Final Rush had great non-rail platforming. Base your stage more on that.
The emerald hunts were my favorite parts of the mod, but there’s a glitch in which sometimes only two emeralds appear in the map (there are supposed to be three), making it impossible to clear the stage. This is unacceptable.
Too many of your stages rely on simple platforming, and that gets really repeatitive. Add unique gimmicks, like crushers, lasers, moving platforms, more fans, inversed gravity, ect, even if this means deviating from SA2's original level design just a bit.
City Escape and Green Jungle were fantastic, visually and gameplay-wise (though do add more textures to City Escape). Mission Street looks both boring and disgusting, but it had perhaps the best level design and enemy placement of the whole package. While this mod is *far* from perfect, it has its shining moments.
Also, about the enemy sprite swaps, it would add more distinction to your mod and would reinforce the whole “SA2” thing. I’m sure the community sees enough Crawlas and Jetty-Syns that something different would be welcome. Even if your sprites aren’t pretty, put them in the game. You can always improve on them later or enlist somebody to help you. Come to think of it, you could also have SA2 style item-boxes (that’d be only a few simple sprite changes) and “breakable” crates (apply whatever qualities a breakable wall has).
Whatever. It’s your mod. Do with it what you will.