This is an interesting idea, but I think it'd probably be too complex in practice. It's already difficult to precisely time your jumping sequences, imagine you'd have to control two characters at a time - that'd twist my brains for sure. Could definitely be added as an option though. I've seen a gamer on youtube ruling Ikaruga by playing 2 ships simultaneously and still beating the game, so I think everythings possible
Since the game was just a weekend project, I'm thinking about uploading the cap file for everybody to use - everyone could just add levels by copying what's already there and add to it, could be a nice little community project and we could all use it as a learning platform. Some of the events, like the doubleJump are copied from other projects (like deadeyes in that case) anyway.
The big layout could be used like a tower, so there'd be different stages to go through and the one that's in there could be level one or two - So Mr. Chung always has quests for you and that door always transports you to the right stage in the layout.
Once there's online we could even test this stuff cooperatively over the net, maybe add one or two more characters with different character attributes to the mix. Sorta like Lost Vikings, anyone remembers that one?
Anyway, just throwing out ideas, I'll be too busy working on Sein and my dayjob anyway, but it'd probably be a shame to just let it die. Zip and Henk deserve some more lovin!