Permanent Death is easy.
You ever play any of the Syndicates?
Where you were an untouchable evil mastermind guy in a satellite or a blimp or whatever, that kidnapped scientists and forced them to design improvements to the cyborg terminator-y trenchcoat agents you sent out to capture more scientists?
Well, yer cyborg agents could get killed, permanently, in all sorts of entertaining ways, actually (running around on fire, screaming, with those last-resort take-one-for-the-team self-destruct nukes in their chest).
But it just cost you some money to replace 'em.
While back at the ranch where yer captured scientists lived (and where most of yer achievements and "level" advancements in the game were actually stored) you didn't really lose anything (although mebbe losing money slowed down yer research and yer ability to shop for and outfit yer cyborgs with the latest improvements, and blah blah blah, I don't remember exactly).
There ya go, yer cake-and-eat-it-too, and that's from before the pentium was even invented heh.
Yah, the whole trick is you just gotta store most of that advancement shit somewhere else, insteada having it all be character-centric.
Woulda been cooler if yer cyborg agents woulda got all beat to hell with bits of robot metal sticking out of their skin and stuff, y'know, semi-permanent injuries and all that, 'cause it'd be all kickass and heroic if a really busted up one managed to finish a really tough mission, but whatever.
And then you wouldn't want him to die, but as long as it wasn't super hard to get another guy into a position to be all cool like that, it wouldn't be so bad if he did, 'y'know, cause then you could get all nostalgic and weepy and shed a tear for poor Agent 05731, 'cause he was just so awesome, man.
And he had to do everything he did with that crappy old Prototype Model of the Persuadatron!
Five miles through the snow barefoot...