You seem to be forgetting a very important part of MK9's story... Raiden's amulet. It would only reconstruct itself in full IF Armageddon was prevented. At the end of the game, there wasn't a crack to be found on that amulet, which means Raiden was successful.
Good writing or not, this is simply a way for NRS to avoid having to cover the post MK3 events all over again. They know those games weren't the best and existed during the downfall of the series.
Raiden only assumed that's what the amulet meant, Dark Raiden was a huge **** and more than likely the amulet could have meant as to stopping Shao Khan from "Winning" like he did in Armageddon. Furthermore, Armageddon being delayed DOES mean that it was prevented, at least for a time as now it will take much longer for it to occur but it still can as it was foretold, since Dark Raiden would have no idea what the repercussions would be by changing the timeline nor does Raiden. All that's established is that Armageddon's path was changed, due to Shao Khan being taken by the Elder Gods, and nothing was done about the main players that actually bring Armageddon out.
Furthermore Daegon, Taven, Blaze, the Dragons, Shinnok, Quan Chi, Onaga and co are so on course as nothing in MK9 stopped any of their events from happening. Another note is that Onaga's return is essential to Armageddon, Shao Khan isn't essential at all for Armageddon to happen.
Heck, Shao Khan isn't even needed for Onaga's return and his departure will make it even easier for those like Quan Chi to steal power in Outworld and put in motion the events that indirectly aid in Onaga's return which was also foretold.
I don't understand why everyone has to over complicate the story mode in MK9. The amulet was "directly" connected to Armageddon. With shao kahn crossing into earthrealm, raiden defeats him, the elder gods step in and shao kahn is taken away(not necessarily dead). By averting armageddon NRS was free to "re-write" the MK continuity. its all pretty simple. it even says that armageddon has been prevented in the MK9 story mode ending. then shinnock and queen-chi step in and reveal some blah blah MK4 derivative scheme. MKX is a whole different story armageddon isn't going to happen. and if ya ask me, that debacle of a game never should have happened in the first place. no pyramid no armageddon period! NEEEEEXT!
Armageddon as foretold long before MK1, Raiden taking out Shao Khan only alters the course but the end result will be the same which is Armageddon, which we know can be stopped and prevented as MK8 was supposed to deal with the aftermath of Armageddon.