Alex Smith by default for me.
I can't see Smith getting worse next year. By the end of the season his top 3 WR's were Michael Crabtree, Kyle Williams and Brett Swain. The 49ers have added Moss (huge wild card) and Manningham, plus there is still the draft.
Urban Meyer famously said that in the first year in a new offense, Alex Smith would be non-functional. He has to know everything inside and out about an offense to be comfortable. Last season he had no minicamps, no OTA's, just a month of training camp before the season started. He had about a week of practices before the first preseason game.
Now that he will have a full season in Harbaugh and Greg Roman's offense under his belt and a full offseason, he should feel a lot more comfortable to start the season. He also should have better weapons. Like I said, can't see him getting worse.
2014 Adopt-A-Lion: Golden Tate
I would say that Mark Sanchez has had to learn 1 offense so far, but I don't even think we can consider it offense.