I think it further cheapen the reapers, which the incompetence seems beyond any comprehension, it cheapens Shepard who clearly didn't know about it, it hurt the original trilogy as you would be out of the loop in a major aspect of the war and at worst is just more prothean technology saving the day.
So that's why I'd like to ask you about alternatives to the ark theory. Or a variation of it that fix those problems I posted. Any ideas?
Before giving you or anybody any idea about a variation of the ark theory, let me remind you of something: in the army (or any military force for that matter), ALL THE INFORMATION IS COMPARTIMENTALIZED. What a General or Admiral knows is of no bussiness of its subordinates. Shepard was/is just a Commander (or Frigate captain), a rank far below Admiral, and Admiral Hacket is far below in chain of command from the commander in chief, from which we know nothing of.
For Shepard to not know a thing from his/her superiors is not cheaping him/her in the least. If anything, is just having a bit of realism.
Now, about variations...well...the "ark" concept could be several smaller ships with seeds, plants, animals and setient species from the citadel traveling through a wormhole. It would make sense and would use far less resources than building a gigantic ship from scratch.