Jim Harbaugh is a really good coach. I don't need to see him in the league for years to know that. John has ridden Flacco's back to an extent. To be fair Belichick has done the same with Brady, Dungy with Manning,etc,etc.
Let me see his bounce back year. Tougher schedule this year. Lot's of things to think San Fran isn't as good as they were last year.
What John has, and I think is being underrated a bit, is several years now of a solid ship. Once Ray leaves, if this team sustains success, I think it's pretty hard not to say that he could go to a poor and make them a better one fairly quickly.
Then again, like you said...if you have a QB with talent, it's hard to see the forest for the trees.