Just finished playing through from the beginning without skipping levels. I'm really stoked on this Alec! This game has a good weight to it(that's the best way I can describe the feeling) that I feel a lot of flash games lack.
I made a running list of thoughts as I played through it:
-red bullets are tough to see on a lot of the backdrops
-solid artwork. I love the colors
-"my rockets will send you back to earth...in pieces!"
-maybe make health pick ups flash. difficult to see on purple ground
-noticed there was no cover system like in the renegade sector games. I found myself using the environment a lot for cover though, so I didn't miss it too much.
-great cheesy one liners
-good checkpoint placement
-human enemies dissapeared into walls when going on conveyor. intentional?
-cool how enemies used conveyor
-hearts get stuck on short walls when defeating the vertical shooter robots inside the base
-some more bass and percussion in the music would bring out the action vibe a bit more. I enjoyed it nonetheless.
-no enemies came charging at me when I was waiting for the 2nd elevator. intentional? I was shooting into the distance so I might have killed them
-music after motorcycle ride didnt stop and overlapped with forest music. After I died it reset and was fine.
-cave music is rad after claw boss
-I like the cave lighting gradient a lot
-great enemy variety except for the last level where I only fought ninjas
-cool to see you refine the Renegade Sector formula this much. It's getting really sharp
-alpha base music is pretty sweet
-2 shots killed the ninja boss. Forgot to reset health while testing maybe?
-loved the breakout-ish blue ball weapon and how you designed the level around it.
-the difficulty ramp was great, but the boss difficulty seemed like it actually got easier as I progressed.
-the bosses only had one attack each besides the giant robot, and his attacks were easy to predict
-the bearillas would get stuck sometimes right after spawning on the sides of the level

The level variety was perfect and kept me going without feeling hung up or bored. I think the only exception was the Alpha Base, but I take it you are still working on that one because it is the last level.
Overall, one of the best flash games I've played. I'm stoked to play it again after you get a bunch of feedback from the community and refine/polish the game a bit more. Thanks for letting me try it out!