They could've salvaged the season with an ending of like "to save the world we have to spread you all out in different timelines or different alternate universes". Something along those lines. Klaus should've ended up with David, Allison with Ray, Viktor with Sissy, etc.
I absolutely loved each and every one of those relationships! I would've been thrilled if the writers had done what you suggested. While it would've broken my heart, I would've also accepted an ending where Five, discovering it was his initial jump that screwed up the timeline(s) and set the apocalypse in motion, sacrifices himself to save the world(s). It would've been a much more fitting ending, considering how almost everything Five did, it was to get back to his family.
And where the heck was Pogo?!
Another unanswered question! I really felt for Pogo in season one, aiding Sir Reginald in screwing up, er, helping his kids by going along with all of Reggie's diabolical plans and likely feeling he had no choice, despite his obvious love for the children (more love than Daddy Dearest had for them). When at the funeral of ol' Reg, Pogo said something along the lines of "Sir Reginald made me what I am today", and of course meant it literally, I teared up a bit.
I also loved season 3's Pogo, taking up with (starting?) a biker gang and spending his time as a tattoo artist and trailer dweller.