Well done on this. You've brought a lot of things together, a cohesive style (art and music), as well as a story and interesting game mechanic.
Fine not having the swop mechanic in the first level. The length of that level felt better then the following levels though.
I'd suggest shorter levels, with bits of story/breaks in between.
Switch mechanic was a great idea and addition, added a new element to the game to keep an eye on when to switch.
Bullet spray from the player was weird at first, but really suited the game in the end. Though That could also have been managed in power ups instead (something for a future version perhaps).
Jam time only allows so much to be squeezed in :).
Think some of the particles from one of the enemies are being launched at a weird angle , and end up hanging around the map until they slowly disappear. Just something to flag there.
Great job on this, lots of work involved.