Having finished my re-watch, I can see why some people had problems with Season 6. The sideways stuff felt like a waste of time ultimately. I would've rather seen more island stuff fleshed out.
I know people question the Sayid and Shannon thing, but if you notice Sayid says that the woman he loved died in his arms and MiB promised to bring her back. No name is mentioned, so that could've been either Shannon or Nadia. They purposely left it ambiguous until we see the end at the church.
All in all, it was still a good show.