1 - Kill off Larrin. Ideally by giving her a Tanith-style death where they just superimpose her face on to someone else and kill her in the first couple of minutes of the episode.
2 - Bring back Fran. Not Fran-Weir. Just Fran.
3 - Bring back Ford for a few episodes.
4 - Give Shepard a cool Die Hard type episode where Teyla and Ronon have to rely on him to be rescued instead of making him look like an idiot. He'd get to be all Special Ops without making silly jokes and wouldn't get captured or beaten up.
5 - Give McKay a girlfriend (probably Keller) and stop treating him like Reg Barclay.
6 - Bring Carter back for the occasional episode as Commander of the Phoenix.