These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Harsher in Hindsight: The little heartwarming moment when Sam and Daniel see General Hammond in the new timeline is made a little sadder with the knowledge that Don S. Davis died between filming his scenes and the release of the movie.
Magnificent Bastard: Ba'al knows exactly what buttons to push to get exactly what he wants. If it weren't for the aforementioned betrayal and SG-1 retaining their memories, Ba'al would have conquered Earth without firing a shot, and we would have loved him for it, and it would of been a mostly safer timeline, albeit under the heels of a Godking who likes western culture.
Rooting for the Empire: Many fans seem to love the idea of Ba'al ruling Earth and secretly wished he'd won, probably because he promised a benevolent governance. It's open for debate how sincere he was. While he certainly didn't want to destroy Earth like all the other Goa'uld, there's a very real possibility he just wanted to covertly take over Earth without having to fight humanity forever, and he'd make them all slaves in the long run anyway.
Strawman Has a Point: Alternate-Timeline General Landry at first seems like a typical Obstructive Bureaucrat determined to stop SG-1 from restoring their timeline. But then he calls them out on their arrogance in assuming that theirs is the "proper" timeline, especially since the Earth of this reality is actually better in a lot of ways. Of course that's all made moot when Ba'al's fleet shows up in orbit.