I wish they'd never taken it back out. I thought the way space exploration was set up in ME1 with small clusters of explored space and large unexplored and hardly accessible space in between was a very cool idea and somewhat different from other franchises. Now that the issue is apparently gone, they are complainng that the Milky Way got too small for them. 
Anyway, on topic: This is definitely one of the better ideas I've seen. It would still be a very long shot send people on a 250 year journey and hope that all the ships systems hold up but I guess it's less improbable than other options.
Still, somehow I can't see BioWare going with this. It's too complicated and would confuse the hell out of any newcomers to the series. Everyone knows that "Wormholes can take us to any place in SciFi". But try to explain to a non-fan why we arrived on this weird hybrid organic/synthetic insect hive thing. Unfortunately, I think that this is gonna be the main concern when finding the entry to the new game, not in universe consistency.
Well, it's Reaper-Tech which (look at the damned Mass Relays!) can survive for thousands of years (note: We don't know how/if the Relays need maintenance, the Citadel does - that's why it has the keepers! - but even then it's old, very very very old and still in very good shape!) so that would not really be a concern (and it's not like they wouldn't send the best people available who might have a chance to fix things mid-flight (that's actually why I think they would need to bring the Quarians along as they've got more experience with space-flight than all other species, simply because there were forced to live in space for so long!)
My problem with the Ark/Black-Ark-Theory is:
Secrecy, I mean keeping the crucible secret (from the general population but also from the Reapers!) was bad enough, but another black project (and one that possibly involved at least as many people? (the people building the Ark (or retrofitting a Collector Cruiser!), the people who guard the place were this happens, the people who are selected for the Ark etc. etc.) secret from almost everybody? Damned, you'd need to be very very very tight lipped about this!
greets LAX
ps: I'd hate to be on the guard-fleet (only to know that I have to stay here, while the selected guys go off to Andromeda...well, if they tell the guards what they are guarding that is!)