Because he's perfect for Langara.
He's brilliant.
He's irritating.
He knew Jonas.
He knows Ancient technology.
And most importantly, he doesn't know everything that happened either.
Maybe McKay was off-world when whatever severed Earth's gate network happened. He's spent years marooned within a small pocket of accessible worlds.
Suddenly Langara has something he desperately needs:
Naquadria.
Jonas and Rodney together would be wonderful because they're opposite kinds of intelligence.
Rodney: "That's impossible."
Jonas: "You told me that yesterday."
Rodney: "Yesterday it actually was impossible."
This season becomes much more technological and exploratory.
And eventually:
Eight chevrons.
They dial Atlantis.
Nothing.
Again.
Nothing.
Finally, in the season finale—
LOCK.
WHOOOOSH.
Nobody speaks.
A Langaran expedition goes through.
And instead of Atlantis—
ocean.
The gate is somewhere it shouldn't be.
The city is gone.
That's your Atlantis movie launch point:
STARGATE ATLANTIS: THE LOST CITY
The movie follows the Langaran team + McKay finding Atlantis.
And Atlantis isn't merely sitting somewhere waiting.
It has been doing something for forty years.
At the end, Atlantis rejoins the larger franchise.
But crucially, the Langarans were responsible for finding it.