Story continuity -10
I'm not sure why people hate this aspect. Lots of TV shows do this sort of thing all the time. And that's if you just use the narrow definition of shifting back and forward through time like this, and not simply switching between two different locations (which every freaking show ever uses).
The only TV I watch is Stargate, and even with just that I see this technique used (and I like it). It allows the story to start in the middle of the action (a classic storytelling tactic dating back to classic literature like the Homer's Odyssey) but also to explain how that situation developed. It also exploits the viewer's curiosity in wondering what exactly happened to cause the situation the characters are in.
I am talking about the Stargate Universe premiere, but also there was an Atlantis Season 4 episode which opens with an amnesiac Dr. Rodney McKay watching a recording he himself made several hours before, instructing him to find a friend of his he no longer remembers, or else he'll die within hours. The rest of the story alternates between the backstory (which also eventually reveals the plan set in motion to fix everything, of course, and explains some of the other things we see in the "present", such as SG personnel hunting their own people!) and Rodney wandering the empty city trying to find Teyla.
Of course it's easy to follow the transitions because the "present" has a hazy video filter thing (I guess to sorta represent everyone's amnesia!) and a sound effect plays and the video flashes to white when it switches back and forth, so the viewer can easily follow.
If the story were presented linearly, I think it would sort of drag (hospital scene after hospital scene) and then when we got to Rodney wandering the halls, it would get old fast. But in the form it's in, I really like it. Just went back and re-watched it last week, even.
As for Universe, both time periods take place in very different locations so it's easy to tell when it's switched. I don't think it would be bad if told linearly, but the way they do it, they get to show both sides of a Stargate during the entire period people are crossing though, as well as have a great opening shot and that whole "in-the-midst" storytelling thing I was talking about.
I think the general problem people have with Raine Dog doing it is that it's not obvious when such a switch between time periods has taken place, and thus it might be a bit confusing until you figure it out. Also the slow update schedule makes it more annoying since each side of the story is moving half as slow as it would if it were the only storyline.