Oo oo, double post, breakingthelaw, breakingthelaw...
How about every time your complete or recomplete a P.E.C challenge, the associated trait would get enhanced. So eventually, a certain playstyle would be rewarded with the optimum enhancement of skills associated with that style. Perpetually sneaking around quietly through entire levels, for example, might be a way to complete the "Advanced Stealth" P.E.C Challenge, and reaching a specified amount of those would allow you to move, super quietly, at faster than normal speeds. And so on for other challenges.
Kestrel specializing in Krav Maga and Archer getting Hapkido or something other, and those style seperations being shown in character animations would be great. Building custom character stats into SC might be too involved and detract from the overall deal. I think we could all go for a larger roster of Spies with varying fundamental differences though.
^ yeah, that's basically what I was thinking. The way I described it makes it sound like a very manual point distribution type system, but in effect it would be like the progressive achievement thingies of the PEC. Every now'n then you'd just get notified that you're agent has increased in experience and your respective skill would get a little faster/quieter.