I hadn't put much thought into story, was treating it more like N Game with just levels I guess. Any ideas?
How about: These little guys are the "foremen" for "their side" of the central nervous system/or brain. Like how people sometimes have strokes and half of their body is useless but the other half is fine.. so these dudes have lost control of their "sides" and need the player to help them work together in concert. It doesn't have to be too specific backstory. It can be bare bones like Super Meat Boy.
I like how the vibe of the game is like it's in an old TV.. so that reminds me of like being in someone's brain or something...
I'd go with the confusing left/right thing... I actually really like it.. I'd map the right dude to a left analog stick (xbox controller) and left trigger/bumper to jump and vice versa for the left dude... WASD and Arrows is kinda yuck.. I'd make it a sit-back-on-the-couch game.
Ever play SUPER SUPER SUPER? it reminds me of that.. my 6 yr old LOVES that game. All that game does is make you hold the controller different directions based on what color you are:
Y=jump, B=move left, X=move right, then you hit a new color and the controls change: Y=move left, A=move right, X=jump
this was SUPER confusing at first.. then I was like.. oh wait, just turn the controller to the right and hold it sideways!