I think one of the main problems I have was the conception of Ultron. He went from "boot-up" to evil AI in the blink of an eyelid. Given that they later played on him being a child of Stark, I think it would have benefitted from some interaction with Stark before formulating his opinions on what needs to be done with humanity. The Thor dream elements were badly handled as well - in the Empire Spoiler Special podcast Whedon pointed out that a lot of Thor got cut because Marvel thought it was a bit too "out there" at this point in the MCU (and, apparently test screens didn't like it) so that element of the story basically doesn't make sense at it was presented. Whedon thinks that there is a 3 Hour 15 min movie in there all told, and given that Amazon already announced an extended Blu-ray hopefully they will be able to release Whedon's full version. I think generally the main problem is that there was too much going on in terms of setting up new characters for the MCU while not leaving enough for the story or the current characters (save for Hawkeye who was owed from the first).
With regards to the Vision, I was a little concerned about his introduction pre-release, however having seen it this was one of my least concerns about the movie - overall I like how he was conceived and the character looks interesting. On the topic of him being "all powerful" because of the Mindstone - is he? What can the Mindstone actually do beyond controlling peoples minds? Also, does he actually know the power he holds? He was, after all, just born yesterday!
On the topic of "didn't Thano's know", I believe the thought was that he put the Mindstone in the sceptre to help Loki in the task of retrieving the Tesseract and if that had worked he would have had two gems. The issue was that the Avengers got in the way. Perhaps "Ultron" AI was in there as a backup?
And regards to the Avengers being "flakes", well the movie is treading the fact that Stark has always been a bit of a flake, amplified by his PTSD after the Avengers (and explored in Iron Man 3). Likewise the Hulk/Banner issue has always been present and this was rushed exploring the issue of Banner basically being used as a tool by the Avengers to wreck destruction but him not having control in that form (maybe a separate another separate Hulk movie would have helped with that one). The tensions and issues were amplified and let loose by Scarlett Witch (who's power also ultimately stems from the Mindstone).