Setting subsequent games before the Reaper war doesn't solve anything. The threat of the Reapers would still hang over everything. Any other danger, threat, storyline the writers came up with would be trivialized by the impending doom the player new was nigh. Imagine if Star Wars Episode 1 - instead of being about the origins of Darth Vader - was about Obi Wan trying to stop an evil corporation from polluting a river on Alderan. The drama would be completely undermined by what we know happens in Episode 4.
Besides, a "prequel" would be, at best, a temporary solution. How many stories would Bioware be willing to tell with the already established lore as a straight jacket. Again, it's best to just bite the bullet and pick Destroy as cannon. Then they'd really be free to come up with new stories.
That would be for the best. You move the franchise past the overarching Reaper plot and the ending and into a position where you can tell many stories linked together by the setting without the Reapers hanging over everything or having a constrained timeline for human involvement like a prequel.
Besides the ending is trash and BioWare has very little credibility when it comes to choices mattering. You wouldn't be losing much by going with a sequel and you have a lot of upside. Sure some people might be angry that they didn't get their circuit board people carried over but do we really know that there are that many people that value their ending choice over getting a sequel?
As for a reboot, if we're worried about pissing people off that is even worse. Instead of telling some people that their ending choice isn't being carried over, you're telling everyone that the events of three games are being wiped out because you can't deal with your own ending.
"Ark theory" abandons the setting BioWare put so much work into building over the years and in service of what? Great we can't revisit Omega, Illium, or Thessia in order to protect ending choices from 2012 that most people have moved on from or view as toxic enough that they don't value it. Why throw out so much good stuff (really the world they built is one of BioWare's strengths) in order to coddle a vocal minority that either takes their ending choice super seriously or is still so mad they don't want the ending acknowledged at all?