Having one of the endings be the sole basis for the sequel (not necessarily the same as sole canon) would be the best way to go for a Milky Way sequel. Of the three endings Destroy is the one most suited for a sequel as the Reapers are completely out of the picture.
The way I'd go about it...
Set 350 years after the events of ME3, long after most characters from the Shepard trilogy are dead, and when the galaxy has sufficiently recovered and rebuilt.
The Geth continue to exist.
The Rannoch decision doesn't end in destruction of the Geth or the extinction of the Quarians. The suggestion that the decision would result in either of those outcomes never made any sense. The Geth are spread throughout the entirety of Quarian space and there are billions of them on servers or space stations outside Rannoch. In fact according to the lore the Geth had mostly left Rannoch untouched since the end of the Morning War. The fall of the planet is a defeat, but it shouldn't be a catastrophic one. Likewise the Quarians losing at Rannoch shouldn't result in their extinction. During the Reaper War there were multiple battles where galactic fleets were defeated by Reapers and yet a portion of them managed to retreat through a relay. There is no reason why part of the Quarian Migrant Fleet couldn't do the same. More importantly a smaller setting with less factions is a less interesting one, and setting up a scenario where whole species have determinant fates and could be extinct based on player choices, does not lend itself well to sequels.
If the player sided with the Quarians, the Quarians are occupying Rannoch and all former Quarian colony worlds. The Geth in and around Quarian worlds were annihilated by the Crucible, but the Geth had enacted a contingency plan to preserve themselves in the event of a catastrophic loss to the Quarians, similar to the Ark Theory. They dispatched ships with Geth servers out into deep space prior to the Crucible firing and these survived the Reaper War. The Geth live in isolation in greatly reduced numbers aboard their own version of the Migrant Fleet, avoiding contact with organic species, and hiding from the Quarians...who discovered the Geth plan and still seek to destroy them. Siding with the Quarians also results in the Quarians returning to the Council as associate members with an embassy.
If the player sided with the Geth, half of the Migrant Fleet was able to retreat through the relay in the wake of the defeat. The Crucible activation destroyed the Geth occupying Quarian space, but like with choosing the Quarians, some Geth escaped on their own arks into deep space. In the aftermath of the Reaper War and with the relays temporarily disabled, and the Quarian fleet stranded at Earth, these Geth won the race for Rannoch and recolonized the system in the war's aftermath. The Quarians settled a few colony worlds that the Geth were not able to reclaim, and 350 years later the two factions are in an arms race, both gearing for another war for control of the Rannoch system. Neither side is part of the Council and the Quarians have become distrustful of other species, viewing the events at Rannoch during the Reaper War as a betrayal.
If peace was achieved at Rannoch Geth survive on their ark ships, and along with the Quarians resettle the former Quarian worlds. The two share Rannoch and have merged into a single faction. The Geth exist in a role similar to that of the Drell with the Hanar, and the Quarian ambassador represents both factions aboard the Citadel.
In all three outcomes the Quarians no longer need to wear their exosuits at all times.
In all three Rannoch isn't a visitable location, because of the varying world states. That wouldn't be a big issue IMO, because any setting in space shouldn't be continually visiting the same planets repeatedly anyway.
If the player cured the genophage, the resurgent Krogan resettle many of their former colony worlds and have rebuilt much of Tuchanka. The Krogan have an ambassador to the Citadel Council and now field the Council's fifth largest fleet, after the Turians, Asari, Salarians, and the Alliance. The Krogan have their first Spectre and there are rumors that a Council seat may be on the horizon. Clan Urdnot maintains hegemony over Tuchanka and the colony worlds.
If the player sabotaged the genophage the Krogan never left Tuchanka and have failed to advance from their Shepard trilogy state. Clan Urdnot was unable to maintain its hegemony in the aftermath of the Reaper War the planet once again descended into tribal warfare. The planet is still a rubble pile and hasn't been rebuilt, and the DMZ is still in place.
Like Rannoch, the varying states of the planet would mean that Tuchanka can't be visited.
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