I feel both defenses will play close or near to the level they have been playing recently. So it will come down to QBS.
Alex Smith has not faced a defense like this before (after being healthy). Alex was hot and cold in the Saints game. 1st quarter (with I believe 2-3 turnovers) he put up points, but he should have put more up against that defense. Then it was dead till the end of the 4th quarter. Then Alex had two very good drives at the end, but do not forget the defense he faced. It will be interesting to see how he does in the back to back games, and vs a tougher defense that is finally healthy and playing at its best.
Eli played fairly well vs the 49ers. He had 1 bad int, and another int that was caused because of a bad route by Mario. It was also a game that was very badly called by KG (remember all those shotgun draws?) but even with that, we had a chance to win, if not for a tip.
Also do not forget (which I did, the team it happened against) they did that onside kick and recovered on 2nd half kickoff. The Giants were also leading the 49ers till Boley went out with an injury, and right after that we got a rookie in the game who blew a coverage, and it gave Davis a long catch/run for the go ahead TD.