I was hoping for a continuation of the alternate timeline, however their was no 'To Be continued' at the end of it. I know because I watched that episode twice. Still I was expecting it and when we didn't get it, then I realized they intended it as it was, but just didn't finish the final scenes where they went back and created the antivirus. It throws us off because we needed some closure after an episode like that.

I don't think they messed with the order of episodes. This story had to follow the Ice planet episode fairly closely, since that's what was making them sick. It was a poor choice not to make it a double length episode though. I bet most people watching it were confused. Its also a mistake to do an awesome episode like that, but not tie it in to the overall story at all. If you missed that episode, you missed nothing that contributes to the story. The writers haven't figured out yet that formulaic television is dead. The new paradigm is to have every episode contribute to the whole, so you feel you can't miss a single episode. The SGU writers missed the boat, and I'm no longer as excited as I was about this show.

As for the Earth soap opera parts, it's pretty boring. I like it only because it makes the charachters less like cutout charicatures, but they really need to liven it up a bit to keep us engaged.