It seems they've finally realized that it's difficult to work out a storyline incorporating paradoxes. Hence, the throwaway about timelines. My guess is that Kiera is slated to return to her original timeline at the very end of the series, paradoxes be damned. But until this arbitrary happy ending comes, they'll play with the more manageable separate timeline approach.
Whether they'll manage to invest this with any thematic interest beyond, does Kiera win (get back to family,) is the question. The family issues revealed for Alec are a bad sign. "Family" has become the Hollywood default for an acceptable moral value. Sometimes it seems that it is the only moral value that Hollywood will deign to even notice.
The real hook in Continuum has been the choice Kiera must make between her family as she knows it and doing the right thing, i.e., preventing her crappy future from coming to existence. But it is very tempting for writers stuck with the limitations of serialization to turn it all into soap. First, the negative possibilities.
A huge helping of the storyline is suffering Kiera. They rewrote Dillon and Vancouver PD into CPS villains, not very convincingly, to put Kiera under arrest for about the same reasons soaps will accuse their lead actress of murder.
Escher's emergence as the real architect of future hell rewrites Alec from ambiguous to hero.
Carlos and Betty complete the martyrdom of St. Kiera by going over to Theseus. Since Julian has a Michael Pitt haircut, it is impossible for him to be anything but an unregenerate villain.
The positive possibilities?
The story is a development of Asimov's The End of Eternity.
Kiera's isn't suffering for the emo of seeing our ideal lay/ideal self/(both?

) crucified by a cruel world. She is confronting failure and the story is how she deals with that.
Escher isn't the real villain now because we've gotten to like/tolerate Alec and don't want (or can't believe) he's the ultimate villain. Instead, the writers are doubling down: Both Alec and Kiera have to choose between their family and humanity.
Carlos and Betty are sincere in choosing the right side.
I wish I could be positive but the consistently negative markers all over Julian (and his father before him and his mother later,) suggest that would be imprudent.