I think you've designed a fun and interesting system here. Definitely original.
One thing that works particularly well is that as you fall you get familiar with the layout of the level, so that once you have to come back up (which is much more difficult since you have to keep both the characters on the rooftop activated), you know what's coming.
I also like that, once you're at the bottom, you get a bit of a resting moment while the hacker can bring your security level to 0. I like that the music changes down there too.
I feel it may need 1 more element in the mix for maximum fun. Maybe having to swing the character from side to side for some obsctacles? I'm not sure.