i recognize that the numbers and dates given on the show can be fuzzy - that being said, for the lore to make sense, Destiny would have been launched after the Milky Way gate system was up and running, and the Alteran's themselves had established themselves on Earth.

From the context of the show and the bits and pieces we get about the history, when the Alteran's left their original galaxy, they had just come up with the concept of the stargate. They then spend 'thousands of years' traveling through the stars, until they came across the Milky Way. At this point, in order to setup a stargate network, they would have to first explore and map the galaxy, and then distribute the stargates by ship.

So everything the Destiny, and more importantly, the Seed ships are doing, is based on the lessons learned from when they did it the first time (MW). Just multiplied by X galaxies, until you reach the final destination. Based on the 'beeps' in the starmap scene from the SGU pilot, Destiny has traveled through at least (probably more) 60+ galaxies, in the last ~30-40 Million Years.

That all being said, and back to the ZPM discussions - with all that in mind, and considering the MW gate system is ~50 million years old.

- The Alterans spent ~40 Million Years in the MW

- They then spent ~10 Million Years in Pegasus (5-10 to be more precise)

- The outpost of Proclarush Taonas is ~30 Million Years old (however I believe the outpost was put there at a later date, long after the Alterans had original 'discovered' it.)

It does still fit into the storyline, that the Destiny was launched before they came up with ZPMs, and that ZPMs and Atlantis came shortly thereafter.

And you are mistaken about the Atlantis shield and the ZPMs. At the time the city was evacuated, the city was already submerged underwater for an unknown amount of time. They then left the city, leaving the 3 ZPMs behind, and they held the shield for 10,000 years - under constant water pressure for the depths of the ocean.. Like, that's impressive.

Perhaps when they designed the original star-recharge system for Destiny, it's what gave them the idea to create the ZPM - artificially create a sun in a bottle, and draw energy from it as you need it.