Re: How Atlantis SHOULD have been..
Off the top of my head: They re-established contact with Earth too quickly.
There was a off-world, colony feel to the show early on which I really enjoyed. Cut-off. Limited supplies. Limited friends because they were new to Pegasus and didn't know anyone.
I think the writers could have played that out for a bit longer.
Then there would've just been comparisons that they turned the show into the Stargate version of Voyager, IMO.
"We travel the world in search of what we need, and return home to find it." - George Moore