I kind of have a feeling that they left it this way so that there is always a possibility of reviving the show or blending it into something else.
After all the crew are off to sleep for 3 years and left us with will they drop back out of FTL on time before the ship runs out of power?
Will Eli get another Pod working? That part is the worst part to leave a fan thinking about....what about Eli!
Who knows... Even though Atlantis finished abruptly after flying all the way back to earth and into San Francisco Bay we still seen the likes of Mr Woolsey and Dr McKay in SGU....... Though it would have been nice to know what happened to Ronan, Taylor and others. Most fans were happiest when both SG1 and Atlantis were running sisde by side in Seasons 9&10 in SG1 and 1&2 in Atlantis....i'd vote that we have something like that back again, where you can get crossovers...happens in shows like CSI as well.