My problem with Season 6, without hopefully going into too much ranting and raving, is twofold:
1) The Flashsideways, while nice and it's great to see all these characters playing redemptive arc again, was just one long, drawn out plot twist that had nothing at all to do with the island plot besides Desmond realizing there was an afterlife and that the island had something to do with it. No ties at all. It negates the timeline speculation of The Incident, plays around with our expectations (which, okay, cool I guess) on how the timelines will have to merge at some point, and is just one long epilogue. Also, did anybody notice the ocean?
2) The main, driving plot on the island. Take out all the sideways distractions. Just remove them. Everything about this plot is so filled with holes, unnecessary red herrings (Ilana, the sword, don't speak to Smokey, Temple, Claire and Sayid, Desmond, Widmore, etc. etc.), the stupidest plots in Lost (Sun hit her head and now she can't speak until she hugs Jin and doesn't get fried by the electric fence; Sayid is alive, but he's also evil, and now he's British, and now he's suddenly repentant cause Desmond's so cool). The only characters I felt had any lasting plot that worked for them were Jack (obviously), Hurley, Ben, Kate, and maybe Sawyer. Maybe Richard, too, while we're at it. And the Man in Black, oddly enough. Everyone else, in a "it's all about the characters" show, got completely shafted.
Well, Lapidus, too, but that's less character development and more Chuck Norris.
tl;dr
1) Sideways plot was just one big, M. Night Shyamalan style twist.
2) Island plot was stupid and full of bad plots.