I have a theory regarding this. My theory is that the Observers are originally from the alternate universe. The reason we don't see them invade the alternate universe in the show is because invading your own past is silly and could cause all kinds of trouble. See below for a more detailed answer with reasonings and even a picture:
I think that the observers in Fringe that take over the past in the last season are all from the alternate universe.
Something that really bothered me in the final episodes is that the alternate universe appears to be completely untouched by the observers. Perhaps they just didn't know about the universe? That seems implausible. They are masters of time and space, surely they would would have rediscovered the alternate universe. Even if they didn't, they would know about it from the reports of the research team which September was part of. They can even travel there with apparent ease, we see them teleport there much in the same way they teleport through regular space.
This leads me to conclude one thing. The observers are from the alternate universe. We know that they are logical and calculating. The chief observer in the future does not want to alter their plans as they have all the probabilities worked out. They will only do something which benefits their own kind. If they were to go back and take over the start of their own timeline, then they could risk disrupting their own creation. Also, if they were to live in their own past, wouldn't it make things worse in the future (less resources etc).
Another thing to think about is why did they choose to come back and take over 2015? Why not earlier? 2015 is only a few years after the bridge is closed. It is possible that it would be the last time the two universes would have any major interaction. If the observers were to go back pre-bridge closing then they would have an effect on their own timeline.
This theory leaves some questions however. First, what becomes of humanity in the non-alternate universe and why couldn't the observers take over there? It's possible that non-alt universe humanity is too much of a challenge for the observers to invade in 2609. In the timeline that the observers are in, the observers could have already taken over the non-alt universe (they would know the outcome of their actions instantly since they are in the future).
Secondly, why does taking Michael to the future end the observer's reign? I think that perhaps he was taken to the alternate universe future (since the future of the non-alt universe would be under observer rule). Donald doesn't explain this to Walter or the gang either because he doesn't think it's important or he doesn't think the others would understand (he knows physics that they can't even comprehend, it's plausible that he wouldn't want to overload their minds with unnecessary details).