First, as other people mentioned, it wasn't a total flop, though it did take one hell of a beating - it recouped its budget, largely thanks to the fact it had little to no advertsing. Biggest bomb of the year belongs to Battleship, which after advertsing and marketing tie ins, lost somewhere above a $100 million, and would have lost more if it weren't for the overseas box office.
As for John Carter, there are two crucial steps:
1) cast someone else as John Carter. Taylor Kitch was an abysmal pick, and even before this year, where the flopping of John Carter, Battleship and Savages, his biggest role was Snakes on a Plane - not the guy you want to headline a movie, let alone a tentpole blockbuster.
I'd recommend Brad Pitt - big name, great actor, and its familiar territory. If you want a smaller name, go for someone really obscure - someone mentioned the guy who played Sawyer on Lost, and that would be a good fit.
2) Keep the name John Carter of Mars for the title. I know why they dropped it (in the last 20 years or so, only one movie about Mars was a box office success, and that was Total Recall - a number of Mars movies were studio destroyers, like Ghosts of Mars or Mars needs Moms). It would work much better here, as it would help sell the concept and reel in people.
3) Market it more! Aside from even a rudimentary advertising campaign, which it didn't get in OTL, maybe a brief animated tie-in on Disney Channel, to help reel in more veiwers. One mistake a lot of blockbusters have made recently is they spend $200 million on a movie concept outside of the popular conciousness. This tanked Battleship, John Carter, Green Lantern, and crippled Tron Legacy among others. Odds are good, had the Tron Uprising and Green Lantern animated series come out before the movies, it would have greatly effected the fates of those movies - why not John Carter.
4) Avoid some of the rudimentary productiuon issues that plagued it.
Even OTL, I loved John Carter - do this and you have a movie a lot of other people would like too.