However, this thread is probably not the best one for trying to justify why the Wraith are morally 'better' than the humans. Not because the argument isn't a compelling one to consider, but because this thread is for this particular virtual series, which isn't a pro-Wraith re-writing of Atlantis.
For one thing, we're trying to keep (as best we can, anyway) continuous with the series. In SGA, while there are any number of problems created by TPTB stylistically that cause issues for fans (let's not even get started on show ships!), in the mainstream telling, the TPTB created the Wraith to be the enemy. And while they did give that enemy more depth by creating characters such as Todd, at the end of the day it was clear they wished the Wraith to remain the bad guys, and Atlantis's humans to be the main good guys, whatever your opinion of them and their choices might be. I, for one, am glad Atlantis isn't full of cookie cutter good guys, because it makes them more complicated and darker characters--which we hope to take advantage of later on.
But bearing that in mind, we made the choice, as SouthernRed says, of continuing the series with general canon as a base and without diverging too far in one specific direction. We can't please everyone, we know this. And while I hope people will enjoy our take on the Wraith, which was a heavily discussed arc, I think we also understand that fans devoted to certain aspects of the series will find issues, as we have often done with the specific parts of the show that we love. I can honestly say that some of our writers had to be dragged kicking and screaming into writing some of what they're writing in order to stick with canon. But we're all making compromises to try and do the best we can.
I don't mean to sound like I'm brushing this aside; I'm not. But my personal opinions of how I feel about Wraith as a fan of the SGA show I don't feel like I could adequately answer in this thread, because it's not really a thread about my opinions, it's more one to answer questions about the virtual series, and the best answer I can give you about the Wraith is that, as a group, we discussed what had been done on the show and the general arc of the Wraith story and built what we're doing from there. We really couldn't 'fix' particular aspects of things (like why the heck the Wraith never built shields into their ships--believe me, I asked that question as I was developing my stories and the canon answer was that they were never there!!), but instead to do the best with what we were given. That was a team decision, rather than an individual's decision, and that's the way our entire series was--it was a series built completely by a group. In some cases, the majority overruled a minority in story planning. But we've done the best we can, and I hope people can appreciate that.