If we have a pick 1-3, i think YOU HAVE TO TAKE HIM. QBs like him don't come around too often, you can groom him for the next 2-3 years and have him just in case Romo goes for the worst health wise(or play wise). The new coach(esp Harbaugh) will probably want to bring in his "guy" in as well.
You never know what the future will bring for the guys you currently rely on, so if you have a potential big time QB staring you in the face, you take him.