Works for me, but Commandos have standardised armour unless it's upgraded with add-ons, so they wouldn't use scout trooper gear which is far inferior. (A scout isn't meant to jump into a fight!) I like the whole customisation idea, if it's quick and easy, so as not to distance it to far from a FPS.
I don't think the whole game should be just about Sev though, he's cool, but remmeber they're an army, they wouldn't abandon their duties just for one trooper, but it'd probably mean that they'd spend a lot of effort trying to find him.
I can imagine a clone would be taken to some lab for genetic analysis for sep bioweapons etc, so there could be a mission to find "any old lab" and then Sev is found!..maybe not so blunt or simple as that, but something that builds up to it.
I am the definition of your defeat.