Revengence isn't considered [url=http://en.wikipedia.org/wiki/Metal_Gear_Solid_V:_The_Phantom_Pain]Metal Gear Solid V[/url]. And it was thankfully called 'Rising' here in the UK instead of 'revengeance', which as you correctly say is stupid. 

The 'Special Abilities' would be like the ones displayed by the various bosses and other 'unusual' characters in MGS, yes. So, they'd have some kind of at least vague explanation based in science or at least fringe science, rather than out-and-out super-powers. I would be avoiding going into what I see as the 'over-the-top' level from Rising/Revengeance, where you have people jumping on missiles and taking out massive robots with swords. 
I'd prefer to limit the abilities to the bad guys, but players will have access to them as well, simply for balance and interest - though they'll be optional. 

I'm glad there's two people interested - I'll keep my mind running and get more thought up for plot. Even if it's just the three of us, that's enough to start. More will be fine too, of course. :) 
And rocketrobie, don't worry too much if you haven't played any of the games - being interested in the idea is enough, and I'll hunt you up some Youtube videos that will help!