I think Atlantis should have done the following:
- Not messed up Ford.
- Not killed Becket.
- Not killed Weir.
- Put more emphasis on the characters rather than lots of action (episodes like "Before I sleep", "Letters to Pegasus" or "The Shrine").
- Not given Atlantis 3 ZPM's or an Ancient ship only to take it away right away. Instead, there should have been a more gradual progression. Eventually, toward the end of the show, Atlantis would be fully powered and fully capable.
- Stuck with the Wraith threat instead of introducing the Replicators. If they had introduced the Replicators, they should have been more like the bugs in SG1. I think the bugs were more menacing than the human form.
- Introduced a story arc whereby the Atlantis team puts together a great alliance of humans (Genii and others) against the Wraith (like what Sheridan did in B5 against the Shadows). Atlantis would eventually play a role similar to the Babylon 5 station. It would become a nexus where humans come together for diplomacy and for coordinating the war against the Wraith.
Basically, I think the show should have focused on the Atlantis team exploring the history of the Ancients in the Pegasus galaxy. The overall story arc should have been that the Atlantis team overcomes incredible challenges to eventually become the true successors of the Ancients: bringing Atlantis back to its former glory, defeating the Wraith and laying the groundwork for what will become a new era of peace for the Pegasus galaxy, thus fulfilling the legacy of the Ancients.