For me, one of the things that bothered me about SGU was the lack of connection to the previous series...and what i mean is this:
presumably, the military personnel were on teams either with SG Command and/or Atlantis. Surely they had experiences or learned life lessons that would have helped.
Now i'm not suggesting they should have had a Lost-style format with flashbacks EVERY week. But if they're going to borrow nuBSG's "feel", why not another genre show?
They could have used ANY Stargate character -- or even none at all. Either way, it would have relayed to me that the characters are truly in the same universe at the others shows, and that SG-1 or the Atlantis command team weren't the only competant people.
To me, the stones were a cheap & convenient way to do earth based stories. (though the last couple were pretty dramatic...it still bothers me how it's very big deal to gate inbetween Destiny & Earth, but like nothing for the stones)