What happened to Lieutenant Ford was unexpected and sad, when the base all turned against him. They killed off a good character.
Colonel Caldwell sounded well prepared. As long as military characters don't turn weapons against their own I admire them. Unfortunately Caldwell's appearance also means that Atlantis is once again connected to Earth, its politics, the IOA, and the secret police state.
Ford has no reason fight the Wraith. He only knows them for less than a year. They haven't killed his family or destroyed his home. I'd rather see him take over a high tech Ancient outpost to oppose the Human military, because it was them who turned weapons against him. Such an outpost would become the only settlement not under Earth/U.S. rule, an essential "Beta Site".