Should the Niners ignore QB in rds 1-3 to upgrade their team? They could then mortgage most of their draft next year (and future draft picks) to move up to nab a franchise QB in 2012.
The 49ers have lots of major holes on this team. In no particular order they need:
QB, CB, LT (depth), OLB or DE (3-4 vs 4-3), WR, FS, Dline (youth), RG (maybe), etc, etc.
They can alleviate some of those needs in FA, depending on the CBA, strike, York's willingness to spend $$$. The Niners obviously have a lot of nice pieces right now, and if they add some veteran players, they have an excellent shot at finally winning the NFC West.
But if they are hoping to draft a franchise QB, they are going to miss out on some BPA options that will fill some big needs. Drafting someone like Mallet or Newton means they pass on a true #1 CB, DE, or OLB. Solidifying the team and adding a veteran QB seams like a better way to win play-off games in the future.
Obviously they should still take a shot at a QB sometime later in the draft, but focus on BPA/need options instead of putting a rookie QB in a position to fail (see Alex Smith).