Agreed. Though one thing I did like about the later seasons was that there was larger focus on the season arc compared to the previous seasons (at least in season 9). Just look at season 7, where the season premiere seemed to establish some kind of major search for the lost city which would carry on through the season, but then it was barely mentioned until the season finale. Or in season 8, when the replicator invasion of the milky way and the downfall of the Goa'uld just started in the first part of Reckoning, and then came to an end in the following ep, with very little build up prior to that. Season 9 just had more focus on the story arc compared to those seasons, and even though the Ori were pretty dull villains, I liked that. That gradual build up from episodic storytelling in the first part of the season to quite heavy serialization towards the back end was part of the reason why I loved Btvs and Angel so much, and it would've been nice to see more of that in the SG shows.
The ships were a major mistake, I agree, but I wouldn't have minded it so much if they had at least held back a bit on the space based stuff. Maybe instead of having lots of uber powerful Asgard enhanced ships there could've just been a couple of ships not much more powerful than the Prometheus we saw in S6.
IMO, McKeller wasn't the sole reason for Atlantis' fall from grace. It all started in season 2 when contact was reestablished with Earth and the Daedalus started to make regular trips to Atlantis. If they had kept the city cut off for at least two or three more seasons it would've added a greater sense of danger and suspense to it all. But of course, far less focus on McKay wouldn't have hurt either. That and better writers.