Oracle, your Shadowrun example is bork.
Cloak and dagger intrigue is supported by the Shadowrun rules just fine. I think in most systems, combat will take up the most rule space, because just like combat IRL, combat is one of the most dynamic events that can take place.
But of course, I would argue that Shadowrun doesn't consider itself a cloak and dagger game how you describe. That is only one aspect of what it can be, and depending on the campaign, even a tiny one. But if you want to run a C&D campaign in SR, it will do so pretty well.
As for 4e, all the classes felt samey to me. Completely subjective. But to use SR as an example (SR3 specifically), mages, deckers, riggers, samurai...they all have some specialized rules, and play quite differently. I like it. Is it easy? No. Is it good game design? I doubt it. But I like it. A lot. At first I thought it was nostalgia, but having recently gone back to playing SR3, I realize that I genuinely enjoy the ruleset.
You can't just tell me that the classes are different. This needs to be supported by the ruleset.