Then 3.0 happened and there's Act 5-10 and it all goes full retard mode, with most of the fundamentals of the world retconned, nothing makes sense if you think about it at all. Really made me lose faith in them as writers.
Not sure what you're talking about here, but it ties in pretty well with the established story from the first few acts and the over-arching storyline that preceded it.
You're returning to Oriath where you originally got exiled from. You get to hunt down the people who sent Dominus/Piety to Wraeclast. As always you fuck things up big-time without meaning to, so you gotta deal with Kitava all of a sudden. By having Dialla contain the rapture devices energy in Act 4, instead of causing another cataclysm like Atziri or Malachai did, you instead go and kill the beast. Unbeknownst to you, that sets free all the gods that just toy with regular people for their own personal benefit. So you gotta hunt those assholes down so mankind may have a chance at some peace for a change.
Powerful/beloved humans ascended to godhood a long time ago and used humanity for their own purposes, so Sin decided to put them into hibernation by creating the beast. Atziri, Malachai, Dominus and plenty of people before that tried to use its powers to ascend to godhood themselves, but since the Beasts purpose was to keep humanity "clean" of such ambition, it just lead to a cataclysm each time instead, creating a new blank slate for humanity until the cycle repeated itself. The people that survived this rapture were turned into the Undying that you meet in Act 3. You're just the first one to break the cycle and actually kill the beast (which you hoped would bring an end to the Corruption). But in turn you set free the gods to use humanity as pawns once more, so you gotta clean up the mess you left behind. Turns out its either corruption or submission to the gods. The first will lead to an endless cycle of rebirth until a new ambitious human arises to try to use the beasts power, which then raptures the world. The latter will lead to humanity becoming slaves to the gods. Sin believes it is better for mankind to choose their own path, so you recreate the beast.
I fail to see how any of this is a retcon to what happens in acts 1-4. I do agree that the story told in Act 5 and onward is much grander, but it already started in Act 4, which set up the entire thing. The players character constantly believes that the things hes doing are for the betterment of themselves or mankind, but is constantly confronted with fucking things up, cleaning up the mess, only to fuck things up even more immediately after again and again. The old endgame storyline was similar in that regard, and with Conquerors we might actually move towards becoming an Exile that fixes shit for once, which will tie into PoE 2s storyline.