San Fran has a better core of players and has drafted Gore's replacement. Atlanta has a bad Oline, no TE, an aging Steven Jackson and Roddy White and a terrible defense. And good luck with Ryan as your franchise QB.
Their core is older and expensive. Next year, the following players will be on the wrong side of 30:
Joe Staley
Vernon Davis
Justin Smith (he will be 36)
Patrick Willis (who we found out this season has had chronic toe problems that finally got bad enough he needed season ending surgery which could haunt him the rest of his career)
Anquan Boldin
Ahmad Brooks
Glenn Dorsey
Antoine Bethea
And just because they drafted a RB to replace Gore doesn't mean he is any good.
Since the 49ers are over the projected 2015 cap, the only way the can improve for the near future is through the draft and they will still have to cut players and/or renegotiate contracts to get under the cap to sign the rookies and get a buffer.
The 49ers are a year or two away from tearing things down and reloading. Maybe McDaniels could do it on the fly like Belichick does, but he is not Belichick and Kaepernick is not Brady which means they will likely have to go back to being bad before they get good. The 49ers' window is closing, not opening.
The Falcons' o-line problems is due to injuries. Early in the season they put their starting LT and C (and the primary back up C) on injured reserves. Their o-line issues are correctable when players get healthy.
The advantages of the Falcons is that they have the cap flexibility to improve fast and they look to be a much better team than their record hamstrung from their coach. If they had a competent coach, they would be at least 7-7 and leading the NFC South.
I when comes down to choosing a team I will always take the team with the better QB and the cap flexibility to get better.