I don't think it's a compelling counter-argument to simply suggest, "it doesn't have to be that way." I also question the relevance of your poll, when in fact it's Obama who will be running for President, and Obama who will be CIC. I know the argument is that people are dumb, but the assumption that Biden will control foreign policy has its disadvantages, disadvantages that aren't represented in that poll (plus I don't believe I've been arguing it will cost him the election--just that it's a crappy pick on message, and a crappy pick for the office). We can see how much that differential shifts when next week's polls come out however.
If "too inexperienced" is a disqualifier for the office of VP, how is it not an argument against an "inexperienced" President? If your VP has a chance of running when your term is up, then choose someone who you feel represents the future of the party. If he doesn't, then make sure he knows he isn't President. If anything (well, "if anything" it should go to the runner-up, but that was nixed) the roles should be reversed, especially in the case where you have a relatively fresh political hand at the reigns: you want a strong President with a promising and independent VP with an eye on holding the Office in eight years; if you want active dissent, it's going to happen in your cabinet anyway. Again, the last thing you want is a domineering VP who thinks he's President. Honestly, this observation has gone from "lol he's like the Dem's Bush" to, "OMG they actually fucking WANT a Democrat version of W's Presidency!" It's kinda spooky.