You raise good points, but time paradoxes are hard to film while making the plot interesting, moreso in multiple episodes.
In many instances, I just shut off that portion of the brain when they get into time travel plots because I know that their explanation isn't going to be good enough so I might as well just take it at face value. It's my defense mechanism. If I didn't have it, then I wouldn't be able to enjoy Doctor Who, Back to the Future, or Terminator.
I finally got to watch Listen and the Time Heist this week. I really enjoyed both of these episodes and feel better about the series since watching the Robot Hood episode.
Listen had an atmosphere similar to the Silence. I enjoyed that feeling, and it had some clever nuanced humor, such as the Doctor taking the coffee cup. Also, I started to get a little bit interested in the Clara/Dan relationship. Despite liking this episode overall, a couple of things did bug me. Why did no one in the restaurant notice the man in the space suit? I had thought that like all things Who, this was one of those things that happen that others can't see, but there's no indication that their descendant (presumably) shouldn't be seen, especially in that get-up. Also, while there was neat closure with the Doctor's obsession with the dream, it doesn't really explain the missing chalk at the end of the opening monologue. The creature on the bed could indeed be another child playing a joke, and I love how ambiguous they left that, but what's the deal with the chalk, unless he's gone all Tyler Durden on us (which could be interesting).
Time Heist had all the whimsy that I liked about the show. It reminds me of my first time watching. I started watching at 11th Hour. Shortly after that (the second episode?) was the episode with the space whales. The Zoltar-like machines throughout the colony that acted as judge, jury, and executioner. Time Heist had that same feeling with such absurd situations. The whole story is very reminiscent of Dick's Paycheck, which is one my favorite stories.