I approve of this far better than I do of 'wormholes' and handwaving, though there are still a few questions that come with it:
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- Just how did they capture a Collector Black Ark? That's the type of story that demands a 'little' bit of detail and action! Was there a great battle to secure this ship? Was it already carrying countless passengers at the time? Did the Leviathans, after being recruited by The Shepard, sever the ship's control from the Reapers and thus the Awakened pilots took those inside the ship somewhere safe? That would be something to see, indeed, and could help explain how the ship was captured.
Imagine this: A team of soldiers raiding the ship in a desperate effort to plant a Leviathan Artifact aboard. Despite the sacrifice of those brave men and women, they succeed and the Leviathans wrest the ship and its crew from their Reaper overlords. Most of the crew dies but some, the original collectors; Awaken. These Awakened remove the Leviathan Artifact (if it can control them like the Reapers did, it is not to be trusted) and, seeing what has become of the world, use their mutated forms to disguise the ship as 'harvesting' those aboard, but really flees to Andromeda. Aboard the ship are various civilians and fighters from across the galaxy: Krogan, Salarian, Quarian, all of them taken from initially for harvesting and now turned into unknowing pilgrims on a voyage into the unknown.They are awakened by the, well, The Awakened, and after a brief standoff are welcomed to Andromeda. These people bring with them memories of the Milky Way and a unified hatred of the Reapers but hope for a new life . . . and perhaps a way back to retake their homeworlds someday.
Why yes, I do think there's a story that can be told about these Awakened, far better than one could tell with Javik. They were twisted into something else but are now free; they are themselves again, but they are also clearly not at the same time. They could be used to explain a much more expedient venture to Andromeda and, I think, would be an interesting case of 'Synthesis' to bring along: Machine and Organic meshed together for deadly efficiency. Collector Companion for Andromeda! *rings the hype train bell!*
. . .Hell, the Leviathans could then be a tool for also bringing the Geth along too: 'Aboard the Black Ark were numerous Geth platforms infected with Reaper Code. When the Leviathans made their move, these Geth too were liberated from Reaper Control. Together they worked with The Awakened to pilot the ship and care for the organic crew aboard, ensuring their safety during the voyage to Andromeda. In particular they cared for their Quarian creators, working to boost their Immune systems for the day they were awakened to a new and potentially dangerous world.'
However it happens, if this is the route they go with, we as the community need to see it unfold rather than simply 'hear' about it. Hell, imagine if that's The Tutorial! Play as someone taking part in that battle, an anonymous, helmeted hero who gives his/her life to free a Black Ark. Once the artifact is in place, the Tutorial Protagonist, an N7, dies (assumed). Cut to opening text wall featured at the beginning of every game. Forward to the start of the true game.
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- The ship obviously have stasis pods aboard, no need to retrofit (processing only occurs at bases, after all no worries about accidentally pressing the 'turn humans into kool-aid' button)? Its suggested that the Collector ship that harassed The Shepard could have carried a great many more people than it was simply by attacking colonies and that it would strike Earth at some point had The Shepard not intervened. In the year 2185, Earth had a population of roughly 11.6 Billion (including on the stations orbiting the planet). Now, clearly the Black Ark isn't going to waltz up to Earth and rescue everyone there, but the question of 'how much space does this thing have' is one to consider when you are bringing a large amount of races and no doubt a stockpile of supplies. . .then there's the whole dextro-levo thing.
--Just how many people are brought total, and how is this divided up? Clearly the Reapers had an interest in humanity because We're Number One, thus we'd have the lion's share of seats, but The races they planned to use for Destroyer ships (Krogan, ETC) are sure to have a sizable portion too.
--How is it maintained? Having a Synthetic (Geth) and/or Pseudo-Organic (Awakened) tend to the ship's stasis pod-refugees is a far more cost-effective plan than a generational 'live ship' and who knows just how 'livable' a ship designed for utility and non-standard organic use would be. They'd need less resources to maintain themselves and would have 'some' knowledge on how to keep a ship going for a long period of time. . .not to mention explain how we are using the same general level of tech.
---Sure the Quarians got by on normal ships, but this is a Black Ark! We don't even know what it looks like compared to a standard Collector Cruiser or if they're the same thing! Black Arks are only mentioned in ME3 and seem separate from the Cruiser ships. All this can be handwaved in comparison to 'how' the ship was taken, however, so its a relative non-issue.