My (Entirely Moot) List of Demands:
1. Keep Atlantis cut off from Earth and force Our Heroes to survive by their wits.
2. If/when this premise runs out of steam, have Atlantis re-connect with Earth but without the assumption that the mission there is worth the security risk to Earth. Atlantis needs some focused mission that makes the risk worthwhile, more than just randomly collecting Ancients tech.
3. Kill off Teyla or recast/rewrite the role so that she isn't so painfully boring.
4. Give Jason Momoa acting lessons and tell him to stop mumbling his lines.
5. Develop the Genii in the direction they were going - villainous, sure, but also simply driven by the need to survive in a Wraith-plagued galaxy. Hang onto Koyla as a recurring foe thru the entire run of the series.
6. Lose the haunted-house cheesiness of the Wraith. Make them a normal society of intelligent beings who wouldn't seem the least bit monstrous if their food source was, say, baked rutabagas rather than humans. Make their "farming" of humans seem banal - they corral humans onto planets not too differently than a large Iowa pig farm - with a political hierarchy and economic system that is orderly and functional, rather than treating them as a bunch of idiots who barge around the galaxy shooting at each other.
I'd prefer that their makeup be way toned down, so that they don't even look too different than human. To have them still feed on humans would be eerier if they didn't look like monsters. The more normal and functional the Wraith appear, the scarier they are.
7. Don't mess up Michael by having the Wraith reject him. The Wraith should treat him better than humans did, accepting that he is a victim and needs help. That would avoid the silly mad-scientist plotline that has been inflicted on Michael instead.
8. Be careful in writing episodes that Our Heroes are not accidentally depicted as utter morons for not thinking things through and making boneheaded mistakes. Examples: not thinking through the possibility that Michael's regression won't work (and therefore they will have to murder someone who appears human; if this is too unpalatable, don't regress Michael to begin with!) and that nonsense where the Wraith got the directions to Earth from Atlantis' computers, that should never
9. Have Shep take off his shirt more often.
10. The "Poisoning the Well" cure plotline was interesting - should have done something with that.
11. NO REPLICATORS! Gah!
12. The Ford problem, hmm. Maybe instead of having Ronin be the big bad muscle-guy, Ford should have been more in that vein - still young, green and gung-ho but also more of a bad-ass. To have him still have to take orders from Shep would have set up more of an equality and contrast in their scenes - Shep is older and wiser, but Ford is better at kicking butt and maybe a bit of a loose cannon.
13. NO RENAISSANCE FAIRE PLANETS! Gah!
14. Hire an entirely new roster of writers and producers, and move production to New Mexico so we can finally have proper-looking alien worlds and not pine tree forests up the wazoo.
15. The idea that Wraith-feeding caused irreversible aging never really worked well as an idea - it means that Our Heroes are not even allowed to be touched by a Wraith because then they'll have to wear aging making forever after - and the writers starting fudging that notion eventually anyway. The Wraith damage needed to be conveyed through some other means than the makeup department so that it could be genuinely irreversible but still a credible threat to main characters.
I know the budget has to dictate alot of choices, so to spice things up, I would have added a race of mutated humans, That couldn't be fed on by the Wraith.
The "Poisoning the Well" cure could have accomplished that. No mutation necessary. At some point, would people from Atlantis be desperate enough to use the cure so that they would have at least some immune fighters? Weir probably would never okay it, but I could envision some situations where it would seem the better option.
Maybe Ford is part of that group and he is one of the few survivors. Do you punish him for doing something so unethical or recognize his value to the team as a result? If Ford is the only immune one, suddenly he has a real purpose in the story. if he was badass enough to take a 50/50 risk of death, that adds an interesting new dimension to the character. I would expect someone like that to get himself killed before the show ends, but until that point, he'd be a great character to have around.