Judging the game solely by its graphics isn't very accurate. Doom 2 was a whole era, while the third part is just a name.
Yes, I also play with imbalances, but I just point it out as a flaw. I just couldn't reconcile myself with In the Wake of Gods. It's just too complicated.
Regarding the outcome: The spectacular dragons read all sorts of nonsense, especially in the early game. And with the phoenix, you can cast antimagic on hydras for dozens of turns, and the battle is easily won.