Lots and lots and lots of details, and you've already greatly devalued continuity.
The endings were designed to end continuity, there is no way to devalue it further than it has been. It has to be salvaged.
So that's what I'd try to do, salvage it.
How would the "destruction" scenario be the starting condition that leads into the control scenario?
Through the plot. Some aspect of the Reapers could be restored and you could control it or it would be used to steer things on to synthesis. I'm thinking of a Shepard-Catalyst subplot idea here. It's not really fleshed out.
That sounds like a fine starting point, if there was zero divergence throughout the trilogy.
Yeah, there you'd just have to dismiss certain options. It has been done before in the Mass Effect series and in Dragon Age. The notion that divergence can be maintained indefinitely has been dispelled a long time ago. It's not that big of a deal.
Anyway, these are just ideas. I like discussing ideas. You can hate them, that's fine.