I will be ranting here, but the issue with the Wraith for me at least was that they weren't much of a departure from the Goa'uld. Sure they had organic based technology but they acted on the same level, they weren't illusive or adaptive in any form they just stuck with an old method which clearly doesn't work. I remember watching an interview with Brad Wright saying they wanted a new big bad that defeated the Ancients but could also be defeated weekly by the Heroes/Heroines, I just had to shake my head at that stupid statement and thought process right there.
Did the Wraith weigh down Atlantis? Because they just repeated what they did with SG1 which was getting stale in my opinion at the time, they just rehashed a lot of the previous stuff. If they had been smart (I know asking for too much these days) then the Wraith would of been a hidden enemy, not one to engage in open conflict preferring proxy than direct confrontation. The idea of not seeing your enemy might seem puzzling but it adds a mystery that has to be solved or revealed by the characters.
Example
SGA Wraith: For a race that feeds off of the 'life essence' (whatever that is, we'll just say rapid cellular division thus giving the impression of rapid aging) they seem to let their 'herd' wallow around in disease ridden, non hygienic population zones, this is the equivalent of letting cattle herd not get treated by preventable diseases. Also why wasn't cloning a method? Surely that would solve all the food resource needs?
My Version: A race that had defeated the ancients but were left with a curse, the ancients introduced a biological agent that crippled their longevity. In desperation they turned to a new source readily available one, the humans DNA was flexible enough to be grafted on, for a limited time they could reverse the bio agent extended their lifespan if used regularly. Turning from soldiers, they became interstellar reapers, no need for battleships or great armies, in contrast to the Ancients, the Wraith kept the humans of Pegasus alive and even seeding other worlds, a twisted form of the Ancients idea. Realizing they had to keep the humans at a low technological level presented problems, they kept their crop alive, secretly advancing health and immune systems yielding much healthier human produce, even in some parts making them more submissive or non aggressive. As for the anti cloning, maybe you could say the Ancients once again inserted a genetic lock in humans preventing artificial cloning (much like how the Asgard prevented Jack O'Neill's cloning by Loki).
What they could of done is switch between the two, have half of the time spent in Atlantis finding out the technology, exploring the City itself and getting into the issues of that and then have the 'away missions' where teams are sent out to gather resources with the looming threat of an unknown bad guy around the corner (i.e. hint at it, be subtle)