It's come as quite a relief to me to find that most of the blogs condemning the flash-sideways and Season 6 in general have dried up, because to me, this is shaping up to be the best season of all! I love how the writers have used the flash-sideways to juxtapose on-island events with those in the parallel timeline, and this is something the writers have not accomplished to their full potential since Season 1. It's become about the characters again, rather than the science-fiction of Season 5. Loved "Dr.Linus". Ben's scene with Ilana will stick in my memory forever. The characters seem real again, because they are making realistic decisions and reacting realistically to situations unlike last season, where I found it a bit odd that no-one freaked out due to the time-flashes.
The only flaw I can possibly find with this season (and it's a very minor one) is the somewhat tacky inclusion of former characters in the flash-sideways, such as Keamy and Omar in Sayid's FST, and finding Jin tied up, which had no relevance at all, and appeared to be added just to reinforce the notion that these characters are still connected in this timeline.
I refuse to believe that the conflict between Jacob and MiB is a straight-forward conflict between good and evil. While MiB has been downright deceitful and ruthless in his destruction of the Temple, Jacob has shown signs of manipulation and clear Machiavellianism, and I think this was explored in "Dr. Linus" moreso than in any other episode so far.
I really hope we get a flashback to ancient times when Jacob and MiB arrived on the scene. It would be amazing.