I agree. Back at the dawn of time when they announced the making of this film, I never heard of "John Carter of Mars" but it sounded so fantastic, so unbelievable. I immediately got excited even though I knew nothing about it. All I knew that it was an old novel and that they would finally bring it to life after several failed attempts. THAT to me was the story right there. Everyone loves an underdog story... well... this is it. The movie itself is the underdog.
And after watching the film... they COULD have done a better job addressing the two different sides and why they were fighting. Most of the time I couldn't even tell who was who. I didn't know it was blue vs red until later.
Also... regarding the title....
They really could have kept the title JOHN CARTER OF MARS. The movie still could have started as just "JOHN CARTER" and end as "JOHN CARTER OF MARS". That would have still made sense and the title would have more of a mysticism about it. When people hear "... of Mars" it might pique their interest. What if they named Star Wars LUKE SKYWALKER.... well at least he has a unique name!