Short post!
Concerning the proposed new system: I like it, or at least I like the idea! I like it because it's sensible. Dummies can't make a quantum computer because they studied for 5 minutes (as PW kinda put it), and a master programmer shouldn't cause The Singularity because he rolled a 6+4 when writing a "Hello, World!" level program.
Concerning dynamic bonus: I'll agree that they're overused, definitely, and I am of the opinion that they should be required to be more specific than they are now. I also had a thought that maybe with the new system they could modify your "level" up by one instead of the roll. This would make it still helpful, and roll back the power of the bonus a bit (with no modifiers as the new system would have, a currently-implemented Dynamic bonus would give you half fives. That's kinda nuts and crazy powerful). What do you guys think?
Concerning stat gains and stats in flesh/robo/synthflesh bodies: I'd just handwave stat gains as a progression element and not think about it too much, or else it gets all weird and nit-picky. As an example, look at...any of the current missions, actually. Assuming they nailed it right now and the mission was complete, they'd receive stat boosts for shopping, eating, and walking respectively. The stats and improved abilities might not have been used at all and they still get better (perhaps significantly better) in the span of, what, a week? You could look at other types of progression systems but what we have now serves its purpose, as far as I'm concerned.
(I could get on board with a general balance pass for robo-bodies, like Radio alluded to. Normal robobodies seem to be very nearly straight upgrades in several categories and don't cost anything, right?)
Concerning "taking a 10": It could be okay, but AFAIK it couldn't be applied to any combat actions in D&D (it's been a while though, so feel free to keep me honest). So you could take a 10 to pick a lock or something but not to shoot a bow or roll a saving throw.
Concerning (potential) stat loss on temp-death: If you want to go this route I might suggest that the victim simply gain less stats at mission competition instead of having existing stats removed. It's still a penalty but it doesn't make it feel like your character has taken a step backwards.