Here's my problem if they are indeed wiping out the Wraith. That will make three races (other two being the Goa'uld and the Ori) who have ruled their respective galactic domains unchallenged for thousands of years. Then suddenly the a group of humans from Earth meet up with them and in less than 10 year those races are completely wiped out? I can accept the Goa'uld, and the Ori pretty much had to be completely annhilated given the way they were depicted, but the Wraith? That's taking things unnecessarily too far. After all, Atlantis is now on Earth, and the Wraith are stuck in the Pegasus galaxy presumably unaware of Earth's location and now having no way of reaching Earth. They're no real threat anymore.
That's the problem with the writing of the franchise. Instead of trying to make interesting bad guys like on B5 and even Firefly, they just make them more and more powerful. That doesn't work! In 15 years we find all this crap that has been laying around that other, smarter races couldn't figure out?
At least the Wraith weren't all powerful, I'd even say... god help me, they were a terrible "bad guy".
However if they kill off their main badguy what will Atlantis movies and Sg-1 movies use for bad guys in the future? The replicators?! *shivers at the thought*
EDIT - I'm glad to see most everyone here agrees on the fact that it's lame that humans fixed everything in 15 years.