I don't believe teams would prefer Peyton Manning over RG3 or Andrew Luck, and the Colts proved that by letting Peyton walk because they planned on drafting Luck.
But some of the factors are interesting nonetheless:
It's not totally accurate to say that teams would prefer non-runners as their quarterbacks. What you're seeing is that in some cases teams value old, proven QBs whose ability to scramble has declined through their careers. It's not that Peyton or Brady choose not to scramble, it's more that they've lost the ability to do it effectively because they're no longer that fast or nimble, and the risk of injury has more dire consequences because they don't recover as quickly. Unfortunately for older QBs, most teams are smart enough to trade savvy, veteran QB play for mobility. This is the point where the Packers let aging Brett Favre go win for someone else so they could take their chance on an unproven run and gunner named Aaron Rodgers. This is why the Niners let proven and stable Alex Smith walk for unproven runner and gunner Colin Kaepernick. Mobility is accurately valued and is valued more than experience and stability.
Younger QBs, those more likely to be good at mobility, are much cheaper. Especially now that rookie contracts are capped and ability to switch teams is limited. Andrew Luck isn't just more mobile than Manning, he's a fraction of the cost. The Colts were right to let proven Peyton go for a chance at bargain basement youth and mobility.
The ability to run and throw well are expensive skills, not in the way of payroll, but in the tangential cost of early first round draft picks. Premier QBs get drafted first, and the conditions that result in that kind of pick are prohibitively expensive. Sure, every now and again you get a Kaepernick in the bargain bin, but not a sure thing like RG3 or Luck. You might have to suck for a whole season to get that pick, and as we know from Dan Gilbert, owner of the NBA's Cleveland Cavaliers, "Losing is always more expensive than winning." The cost in team culture and morale and the loss of being a premium recruiting destination for free agents is probably right up there with the decreased viewership, merchandise sales, advertising dollars, and ticket sales. Instead of "Losing for Luck," it might be better to do what the Chiefs did and cherry pick a proven commodity like Alex Smith (or like the Broncos did with Manning).
The Chiefs and Broncos (and before them, the Vikings with Favre and the Saints with Brees) opted for older, less mobile QBs because the cost of drafting premier, mobile QBs is too high. It's cheaper to pay the higher salary of a wily old vet than it is to pay the cost of tanking for an early first draft pick to get someone like RG3 or Luck.More questions on NFL: