They made the ending that way because there was supposed to be a direct to dvd movie made that would have further went through the story. I believe they were going to have to get Atlantis back to the pegasus galaxy or something like that. Unfortunately, MGM pulled all funding to the SG franchises, and here we are.
Definitely miss this, SG-1 and Universe. Although I love re-watching SG-1 and Atlantis the best.