Wraith technology is based on Ancient technology, and very well could have been based on the "original FTL" IE, Destiny. I tend to believe that with the sensor tech available to the ancients (they did detect the background signal btw), if they could have used hyperdrive, they would have. I believe that Desitny's FTL was simply used because it was built long before the current star drive or hyper drive was developed. It could very well be that destiny is simply a failed experiment, or even a "mapping" device. No one knows for sure, just that it's pointed toward some signal.
As far as the seed ship speed and the 2000 year thing: well, simply put, they would have built many many seed ships. Maybe they built themselves after they found enough resources? (early replicator tech maybe?) The simple fact of the matter is that the seed ships would have harvested materials, and dropped gates, and other seed ships would have bypassed this on to the next galaxy. So maybe two or three seed ships is all you would really need to "stay ahead" of Destiny.
By the way... on the topic of speed... remember the SG-1 episode where the replicators took over the Goa'uld ship and increased its speed to 800% of normal? I don't know how fast that is, but I would be willing to bet its faster than the Asgard ships. And since the replicator tech is based on ancient tech.. it would be safe to assume that the ancients were capable of traveling far faster than Destiny (towards the end of their existence that is)... could it simply be that they just used a faster ship and completely the mission long before destiny ever could have? They had star drive, why not just map the destiny coordinates, then jump there. then jump further, and further... etc...mission completed. whats the point in destiny then? SGU ended partially because there is no good, semi-plausible story line. any "mission" would of been completed and logged in the database. (unless it was super duper secret and dangerous like the weapon Rodney used to destroy that solar system.)
