Two of my favorite characters from last season have simply disappeared from the show with no explanation.
First, Tex. Sure, with the doc gone there is little reason for him to stick around, and they did show him setting off to find his daughter at the end of last season, but I expected we'd follow that storyline to it's conclusion this season. Nope, it's like he walked away and fell off the planet. Nobody even mentions him in passing this season. The Australian SF guy (who is pretty awesome) seems to have replaced his function character-wise.
Second, the dog. Granted, the dog had only cameo appearances in a few episodes last season, and it really doesn't make sense to have him aboard ship given this season's plotlines, but again, just gone. I'm going to write a story in my own head where Tex took the dog with him and they wander the wasteland of the central U.S. rescuing people from bandits and righting wrongs like some kind of U.S. version of Mad Max. That might even make for better TV than the actual show...
I do think they've done a decent job with moving the focus of the show from finding/protecting/distributing the cure to this season being the caretakers and peacekeepers of the new world order. Obviously there is enough infrastructure left in the U.S. to make cure distribution and societal cleanup/rebuilding a task for others to handle, so our gang gets to be international heroes and peacekeepers. Of course China is cast as the villain, they are the only "boogeyman" left with resources to threaten the U.S.. It would have been cool to spend some time touching on rebuilding efforts worldwide, but I suppose that's just not action enough for this show, which is understandable. Still a nice guilty pleasure of a show with several actors I like in the cast.