you dont watch very much pro football do you?
OK, I'll bite, since I don't follow the NFL closely anymore. (Can't stand the prima donna lack of discipline, the tattoos, the look-at-me shows, and the long hair.)
Who are these QB's that are at the pinnacle of both running and passing ability? When I mean "run" I don't mean "scramble" to avoid contact, or a situational play on occasion. Have these QBs been doing it for a long time to demonstrate this as a viable approach to using a franchise QB?
The great passers in my mind have been guys like Favre, Marino, Brady, Manning, Roethlisberger, Brees, and so on. Some of these guys could run, but they were not used as runners. These are not guys putting their head down as ball carriers against NFL defenses, at least not to any great extent. If there are QBs out there now that really are being used as runners in a QB run option offense, then it must be a new thing, or they are doing it to the detriment of passing. Despite rules changing to favor passing, these guys are not on any all-time leading passer lists. And I wouldn't expect them to get there either, before they get banged up.
When your head and shoulders are taking a pounding something is being given up in your ability to throw. The run isn't free to someone who must think, keep their wits, read defenses, and throw accurately. If you run a lot as a QB, I'd say that a true passing pinnacle has not actually been achieved. You may be helping the team with that run, or so it would seem, but it doesn't come for free. It comes at the cost of something else that you may not be able to definitively quantify.
Robert Griffin III is a classic case of what can happen when you run your quarterback, to illustrate an extreme of what I'm saying here.
Maybe rules are changing to the point that you can't tackle the QB anymore. Then it would make sense.