One of the aliens on Defiance said that they spent (a) hundred(s) years in cryo getting to Earth. I don't recall them saying anything about their ships having faster-than-light propulsion, but that still works (and works better since it appears FTL is a pipe dream without cheating (aka warp drive

.
The thing is, with time dilation occurring as you approach the speed of light, time on the ships would slow down relative to time passing for someone not on the ship. This means that your "scout ark" could have arrived at Earth millions of years ago and, from our local frame of reference, the rest of the ships just got here in 2043 (or whatever date the show takes place).
So these aliens discover Earth through their telescopes and see it as habitable. They send their scout ship to check it out, which takes millions of years from the aliens waiting back on their home world frame of reference. When the scouts arrive, they see nothing but dinosaurs and shit, so they send a signal back home saying, "Hey bros, this planet is perfect, come check it out." So the fleet takes off.
The fleet takes longer to get here because it's a lot of ships and they have to stop for gas and piss breaks along the way. By the time they get here, humanity has evolved and there's no sign of the scouts they sent in advanced. What happened to them?
Well, the scouts figured they'd get a jump on things. They didn't want to fuck around with no tyrannosaurus rex, so they drop an asteroid on Earth and wipe out the dinosaurs. Then they head down and start fucking around, genetically altering life so it would be more compatible with their diets, or some shit like that, inadvertently changing life on Earth forever. Then some shit goes down and all the aliens die off mysteriously.
So the aliens end up being responsible for the creation of humanity, in a round about way via evolution, but their buddies have no clue what the hell is going on since they're all sleeping while their ships head this way. They show up, see that Earth is now populated by some weird alien race that didn't show up through their telescopes. They open a dialog with the humans and the humans are like, "fuck you weirdos", so the aliens figure "Hey, we're outta gas, and these human things are primitive. Let's fuck them up and take their shit!"
So the aliens invade and there's a big war. Humans are losing, but then something happens! Their ships blow up for
mysteriousreasons, killing most of the aliens. Stranded, the aliens are now stuck on Earth, and the planet is all changed and shit since they used their Genesis torpedo to terraform Earth (when it apparently didn't need it).
As far as I can tell, this fits with the story that was in the pilot, what little they mentioned and from what I remember.