Everyone is assuming that Seed ships were build on Earth?
It is said that Destiny was launched from Earth, but we have no way of knowing where the Seed ships were built.
From episodes of SG-1, the Ancients appear to have passed through the Asgard galaxy (Ida I think) first, then reached the Milky Way and then on to Pegasus. The stargate created by the Seed ships are the oldest generation we know of, from SG-1 when O'Neill first got the ancient database in his head, the Asgard galaxy stargates are the same type as the Milkly Way galaxy stargates.
This indicates that the stargate design used in Stargate Universe by the seed ships were created before the Ancients ever went to the Asgard's galaxy. This would mean that the Seed Ships would have likely been launched before the Ancients ever entered the Asgards galaxy or came to the Milky Way as the seed ships would probably be using the Milky Way model stargate instead.
The older stargates on Stargate Universe are limited by range, they may also not be compatible with the newer models of the Milky Way and Pegasus galaxies, meaning that the gate on Destiny was already an obsolete design and only put Destiny to work with the seed ship stargates already on planets.
Also in an episode of Atlantis (last one I think), it is stated by McKay that Pegasus stargates override Milky Way Stargates, this might also happen with Milky Way gates affecting the seed ship style stargates in some unknown way.
Destiny may have simply been built to carry on the "creation of the universe mission" automatically.
The design of the destiny may simply be a larger variation of the Seed ship, we know from Stargate Altantis that there appeared to be at least 3 variations of Aurora type warship and 2 slightly different Atlantis City Ships. The Destiny would have had to have been built with certain technologies, capabilities and design features to match the Seed Ships, remember that the Destiny was able to dock with a seed ship twice.
We also have no idea of how long the Ancients spent in the Milky Way and Pegasus galaxies. In the Milky way galaxy, the Ancients appear to use stone structures for buildings, yet the few outposts and structures we see in Pegasus appear to be made of much newer materials like steel and concrete like substances.
We also all assume that Seed Ships only had faster than light drives, it is possible that the seed ships used hyperdrives when travelling between galaxies! As there is no need to plot for gravity wells in these areas allowing for hyperdrive between galaxies, this might also explain why the smaller seed ships have massive power reserves compared to Destiny's. The Ancients would have likely had hyperdrives before all of this, however there is no real way to know, except the Ori who the Ancients broke away from had to use a supergate to get to the Milky Way indicating a massive distance between galaxies. From the SG-1 film Ark of Truth, there is a scene when the Ancients leave Celestis where an Ancient has drawn an image of a stargate in what he says is his notebook.
This could mean that the seed ships placed the first model of stargate in every galaxy between the Ancients/Ori galaxy and the Galaxy the Destiny is in. Then followed after the seed ships at a later date replacing the seed ship gates when they got to a new galaxy. We also dont know if there were other types of stargate designs between those of the Seed ships and the Milky Way models.
All these factors may allow for the massive times between the launch of the seed ships and Destiny.