The concept of a QB that can run at a high level but also operate a successful passing game is not new. I think Kordell Stewart started as the Steelers QB around 10 years ago. The college ranks have been producing plenty of QBs with these type skills for many years now. Yet they largely haven't caught on in the NFL. One reason for that, IMHO (my theory), has to do with the running itself. With pro coverage schemes so intricate and effective, the ability to operate a successful passing attack against the better competition of the NFL has a dependency on rhythm and a high repetition of doing it. A QB that has a high frequency of runs will likely miss those critical reps needed to not only operate a high yield passing attack but aid in taking his game to a higher level. A truth of the NFL, whatever you do in the NFL as a rookie probably needs to be markedly better in year 3 and year 4. Put another way, if you are doing in year 3 what you were doing in year 1, your success is probably waning (again, just a theory).
Another reason, which the OP touched on, when you have large wrecking machines like Ray Lewis in the waiting, the amount of hits you accrue will effect your physical health -- especially considering the unique punishment QBs already take (standing in place, sometimes in vulnerable positions while blitzers hit you at high force, sometimes blind siding you). Even with the near coddling QBs are afforded by the NFL (which is a fact that will help RGIII to a degree), the unique punishment by big and ferocious defenders is going to be significant.
RGIII is probably running the dual threat better than just about all others to date (in part) because of his sleeker size (also in part because he is also producing very well in the passing game). He is just about as agile as it comes for someone at the starting QB position. But the sleek size makes his future durability a very iffy thing (far too quickly if he doesn't learn to duck). Now a player like Cam Newton? His significantly greater size has a better shot at longer term durability. If he can elevate his passing game abilities and his team gets a defense? I like his chances better. But his passing game ability, his ability to protect the ball, ability to complete the third down throws at a solid frequency has got to be elevated. So far Cam Newton year 2 appears to equal Cam newton year 1.
Disregarding the mediots belief that this is the skillset of all future QBs, I am not yet sold on the RGIII mold of QB. You have to appreciate the level of excitement a rookie! adds to the game yet has there been a QB of that mold that has put together more than a successful season? A bit early to declare this skill set the wave of the future given that the 4 arguably best teams in the league are manned by the drop back passer (Atl, GB, Den, NE). With that said, this skillset type QB is providing some success quickly, getting positive attention for the team, putting butts in the seats/people in front of the TV. With enormous pressure to win right now and the seemingly slower process to build a high caliber team around a drop back passer, IMHO there is going to be plenty of teams that go this route in the next few years. If I then see these teams have the high level success semi akin to the Patriots or GB or PM teams? I'll then believe the mediots (I dislike having to agree with the mediots on anything though).
I think the Rodgers / Luck / Russell Wilson style is ideal. Primarily a passer who can run if needed. All of those guys Average under than 6 attempts per game. As long as the QB is smart enough to keep himself healthy it's a big advantage for the offense. RG3 needs to get better at this no doubt.