Thing to keep in mind about Shannahan and the 49ers: Falcons offense has Matt Ryan, Julio Jones, Sanu, the top 1-2 RB duo, and a very good OL. 49ers don't even have a real QB.
As long as the Falcons have their main guys, the offense will do well. Maybe not historically great like this year, but the Falcons offense was never terrible. Matt Ryan is a top 5-10 QB now, and no way 49ers get that this year or the next 3 years because it takes time to develop one, and franchise QBs don't get traded or go to free agency unless something is wrong with them. 49ers also have one of the most inept owners in the League, where Arthur Blank is widely respected and players and executives enjoy working for him.
Our defense was young this year, and I would assume we'll get more talent this offseason. Falcons are definitely in a good place to continue the success.