There was that whole Peter and the Irish plot line that just went nowhere. With Peter inexplicably loosing the girl in an alt future. She's just gotta reappear later somehow, though I don't see how there could be any continuity to her character.

Then there's been no explanation why the whole Linderman led coalition existed and was crushed. Unless we are supposed to accept that is was

This whole working with alternate time lines, changing either the future or past is just too convenient for the writers. I just hope there's a plan to tie it back together before the series gets canceled.