Keep:
Rush - He must be relegated to a 2nd in command role, which allows the character to continue to be an antagonist.
Greer - Put him on some meds; the man seems psychotic. Or kill him off, I don't much care.
James - She's likeable and has potential to play a strong female role on their SG team.
TJ - Put her into med school via the stones and turn her into an actual doctor. Duh.
Chloe - I could see keeping her if Scott leaves. She performed well on the Lost mission, but her stupid relationship with Scott seems to hold her character back. Give her some skills, and put her to work.
Lose:
Young - He's a loose cannon, and not in a good way. Send him back to Earth or kill him heroically. Definitely end the BS with that wife of his.
Telford - Whether or not he's really such a bravo foxtrot as he came off with Telford's wife (or whether that was his Alliance brainwashing), the character is too damaged by those actions. Kill him heroically.
Scott - He's bland, and he's got the perfect excuse to leave (his son) if they can gate home.
Eli - He's got a great reason to go back home (to watch his mother die), so put him in a consultant role back on Earth. We don't need a nerdy Rush Jr.
Wray - She's done little but proven herself to be an incompetent, petulent character, and I'd like to see her die horribly. It's a pity that she wasn't eaten by the aliens in Time, during the last iteration, so that the crew said, "Well, we've tried this in a couple timelines, and we've got our venom. Guess Wray was an acceptible loss. No need to try and get everything perfect, you know."
Bring on Board:
Sheppard from SG-A. Seriously. Make him a full Col. and place him in charge of the mission. The show needs a little of Sheppard's style to loosen things up, but also to provide the crew with actual leadership. No need to keep the captain on the ship - send him off on SG missions. Worked for Kirk.
Amanda Perry, cure her of her illness, but trap her on Destiny as a result (see below). She brought out a much-needed aspect of Rush's character.
Destiny - Give the crew control over the ship. Bring in McKay and Jackson to work with Rush (via the stones) and get the bloody thing working. Ramp up the enemy threat level. Give them one gate home and one gate back, then use it to eliminate the dead weight in the crew and to bring in fresh blood.
Set it up so Destiny has primitive nanites that can cure a small range of ailments (do not turn these into miracle nanoprobes!!!) if activated by the computer, but the nanites will only work onboard the ship. That's how Chloe was healed, but if Chloe subsequently left, her wound would reopen and she'd have to re-heal her gunshot wound herself (that would be an interesting episode, btw). If Perry's condition is cured by the ship, she's forced to stay aboard or the cure will shut down and she'd be sick again. Say Whats-his-face who used the chair and disappeared was zapped into the computer (and was thus the one who saved Chloe).
Plot lines - More aliens, more ships, more of a focus on the SG missions, not the shipboard drama.
Contact with Earth - allow one dial out (first one, dump the alliance soldiers and the crew listed above) per year or two. Perhaps have a a gate capacitor charging up that can be used as an explanation. Allow one dial-in, perhaps from Atlantis, to resupply and exchange crew. Use the stones more intelligently, and bring in interesting guests from the other shows.
I want to see
Jeannie Miller again, too.