Because the Ark Theory either 1) eviscerates the established lore about our cycle's level of technology and common sense and/or 2) requires a massive Deus Ex Machina in order to grant us intergalactic travel. If the Ark was built after the Reaper War it would be a different story since then we'd have several years or decades to either reverse engineer Reaper corpses(Destroy, Refuse) or the Reapers help us crack it(Control, Synthesis), but there is no logical way they could do it in less than one to three years.
So while changing or combining the endings may seem destructive to the endings(I find this debatable), the Ark Theory is destructive to the entire franchise.
The seeds for the Ark theory are already there.
The Prothean, I forget his name, Javick or something like that, was in stasis for a very long time.
We don't yet know how long this trip took.
This could have been the work of the Asari's, who diverted their own resources to it.
Is there a decent amount of Dues Ex Machina there?
Sure, but not completely. The seeds have already been planted by some of their previous choices (the Prothean capsule and the Asari council saying that steps need to be taken to ensure continued civilizations).
And changing or combining endings are destructive by definition. It's a tautology. If you change on ending, then it's no longer an ending. If you combine endings, then you by definition change the previous endings.
Regardless of what we felt of the ending, it was designed to be an ending. All the postscript adult telling the child the story couldn't make it any clearer.