One that always got me is: why does no one think of using the transporter as a weapon? Once the enemy's shields are down, you can just beam the entire enemy crew into space and have a relatively undamaged enemy ship to capture.
It also doesn't suffer from "Cool Technology in one episode -> never heard from again" syndrome, to give another example of an improvement over Star Trek.
If you've never watched it, I recommend it. It sort of dies with a whimper rather than a bang (opinions on the spinoffs are mixed), but SG-1 was very good for a very long time. Mainlining the first season episodes without commercials and in sequence is really a spectacular experience if you can stomach the "time wastiness". The first couple of seasons in particular really captured the sense of humans being thrust extremely suddenly into a new, huge universe without guides very well.
It's well established that all Goa'uld have the vast knowledge required to pull miracles out of their hats at will. They can and will punish any defector who doesn't have a huge advantage. Just look at how they allied against Anubis, when he made his bid for supremacy.
The Goa'uld are not pathologically incompetent; they're just wary of being disruptive.
My theory is that there are some rules of war that most people with transporter technology follow. We've already seen examples of similar conventions in Trek; for example those banning thalaron & subspace weapons (Nemesis & Insurrection movies respectively).
I think a more realistic theory is that the script writers simply had to draw a line somewhere and ignore the obvious inconsistencies from that point, or they would have never finished an episode.
It was an entertainment TV series after all, not a scientific paper...
I do agree anyway that many episodes were real turds. Personally I hated every single one with "Q" in it. Often those were not even internally consistent.
The trick is doing it right after it starts assimilating the ship, but not after it's successfully done so and suddenly turns on you and everyone else in the sector...