The thing that wrecked Season 3 and hurt Season two was "idiot plotting," i.e. in order for the plot to go forward, the majority of characters has to be idiots.
In season two, Charlotte and William didn't have an anti-Ford fail-safe installed. Dolores outwitted them at every instance, even when the "real people" outgunned them. This, with the excellent writing as counterpoint, stuck out like a sore thumb. Also, why didn't they just put everything on a pearl and go? Idiot plotting.
Season 3 was even worse in that regard. The plot holes were big enough for a battleship to pass through, and while there were bits an pieces of genius here and there (plus cool fight scenes), they didn't balance out like they did in season 2. Seeing Charlotte/Dolores become Delores/Delores would have been really interesting. But they skipped that part and just had our mechanical heroine become mechanical supterbitch who can do anything. It was all too easy.
I understand some idiot plotting might be necessary to keep the story going, but in Season one at least, it wasn't noticeable. In season 2, it WAS and in Season 3, it overwhelmed the whole thing.