Here's my Stargate Plan.
Step 1: One final SG-1 movie that ends their story with definite finality. Teal'c dies. Jackson disappears and never returns. Cameron commands the next 304. Vala gets bored and moves on with her life. I don't know the details but the final shot would be O'Neill and Carter sitting by the lake with fishing poles and full-on making out. Sounds like slashfic but whatever to end their story.
Step 2: Atlantis. Biggest thing is I'd demand some better character development. The entire cast is game for meatier stories so I'd make my writing staff step it up. The thing they do well with Stargate is pack a lot of story into 44 minutes so it shouldn't be a problem. One thing that would help would be more B-stories. They rarely do that on this show.
This is a fun show that's doesn't have heavy material so I'd keep it that way. It's basically swashbuckling adventure. The only thing missing from this adventure yarn is romance. I'd get that going and not that Kanaan mess or childish Keller/McKay stuff. More Kirking for Sheppard. I'd have Keller hooking up with people on the base because she likes to have fun. A party girl who can be a competent doctor is an interesting place to take a character. I'd have Ronon get his heart broken by someone because he's a HUGE romantic and Momoa would act the hell out of that. And I'd be tempted to make Lorne gay because Torchwood has shown me how fun that is to watch. Who's to say. Finally, I'd introduce the idea of families to Atlantis by marrying off Woosley. No kids because I don't want this to turn into TNG. Give him a smart, tough and loving wife who's not a ball-busting bitch like Keiko O'Brien was. But it would be nice to see a mature, loving relationship in sci-fi that's devoid of drama and it'd give Picardo some great screentime.
First, I'll say that I'd keep the Wraith. They are good villains. But I'd retcon them back into S1 & S2 Wraith with queens and cullings. I'd wrap the Michael stuff up in a two-part episode and in an intentionally Deus Ex Machina sloppy fashion so it's an obvious mea culpa
to the fans. Then I'd forget that scientist types like Todd and the guy who blew up Midway existed. The Wraith are better as an infection instead of a villain.
Then I'd bring in a new villain for the mustache-twirling. A fun race. An ostentatious monarch and his royal court who want the Ancient technology from our heroes. Think Genii but without the lame Communist white trashiness. This race would be a massive threat to our Heroes with their superior firepower and unpredictable leadership. Throw in a princess with a thing for Ronon or McKay, a love/hate respect between the monarch and Shep and a court who is constantly trying to overthrow each other and it would be a great fun villain for Atlantis. Think Princess Ardala from Buck Rogers mixed with The Centauri on B5 and you get the idea.
Finally, I'd throw in an intensely serialized romp of a season 6. Every episode would end connect with the next, much like Angel S4. One long story arc for just one season. All of the above elements would play into this season.
Step 3. Stargate Universe
I'd continue to try to develop this so both shows can run concurrently.