It has to be both, out of necessity.
My problem with your assertion is not that there won't be the threat of a pass, but that there won't be much threat of a pass. There are very few guys out there with both the ability to run like a RB and the ability to read defenses, make decisions and hit on complex passing attacks. Kaepernick, to me, is the perfect example - he's good when his choices are primary read or run, but defenses can scheme to clamp down on a primary passer, and teams like the Rams have shown that you can put a Barron/McDonald/Ogletree type to "spy" the QB and whomp the crap out of him if he pulls it down.
I think this is the major difference between your POV and mine - I think there are way, way more QBs available who can make reads and throws in a moderately complex passing attack than there are who can reliably complete, as they say, "all the throws" and also run like a deer. RG3 was the one I thought most likely to be like that, but his injuries and inability to evolve the passing game have left him pretty much useless.
If a team takes away a guy like Kaepernick's ability to run - and they will - he needs to be able to operate a reasonably efficient and effective passing attack. Those guys are rarer - yet, admittedly, more effective - than guys who can stand in the pocket, survey the field, and put the ball where it needs to be.
My opinion is that you're chasing a unicorn, whereas good pocket passers are just fancy horses - less awesome, but also less mythical.