I completely agree with you on #1 and #2, but for #3, I'd add that Torri's and Paul's characters were basically the foundation of the show. Without them, the show just wasn't the same and it became something that it wasn't. It fell apart completely. The "Ghosts in the Machine" episode was the final nail in the coffin for SGA. Also, I'd say that not sufficient episodes dealt with the exploration of the city itself, the history of the Ancients seen in "Before I Sleep" (assuming here there were various groups of Ancients all across the universe) which lead to the lack of the actual mythology that actually resolved around the city and the Pegasus Galaxy themselves, as well as the possible plots where certain characters could be connected to the city more than they can think (Teyla, Ronnon, Wier and maybe Ford). Some missed opportunities for great storylines that could enable for at least 5 more seasons for Atlantis.
SGA had a great set of cast members, but TPTB obviously didn't know what to write for their characters, i.e. for the characters they developed. But that's probably MGM and Syfy to blame for, since they wanted TPTB to run TWO shows at once, thus preventing them to really & completely focus on the series since they had to still run SG-1 AND give it the "main show" treatment. SGA was always going to be a side-show, the #2 show, even if it got the chance to run for a couple of more seasons. I mean, even SGU got MORE attention by its creators and was treated BETTER and more seriously since they made the show resolve around the characters.