Software quality declined, sales of Amigas declined... Doom was released, the Amiga had no hope by then... The ball was already rolling... Commodore folds, end of story.
Yet, in truth, neither game has ever been beyond the reach of a modestly expanded amiga.
I always found it highly ironic that the Amiga got an official Quake port (and an unofficial one prior to that) long before Doom became available for it.