I'm a big fan of the 'conflict over rebuilding relays', with a post-time-skip conflict centering on a the prospect of a new relay network and a struggle between those who want to rebuild the relays and Council system (and, in essence, place themselves at the top of the pecking order) versus those who oppose a new relay system (vested interests in the slow-FTL trade routes, those fearful of invasion or domination). Call it a post-relay Council vs. Terminus war.
Such a conflict, since it would arbitrarily decide what sectors of space it was in and what relays are repaired or not, could pretty easily reflect the non-ending choices. Since there's no reason to return to the Geth, Quarians, Krogan, or Rachni as primary plot-relevant species, they can largely and easily be kept off-screen regardless, with token representatives to reflect their new role. Geth/Quarians, for example, could be largely isolationist at Rannoch as they pursue self-development/repopulation, with only a relatively few travelers reflecting their role in the wider galaxy (helping evacuate AIs to reduce conflict/hunting AIs to prevent AI conflicts/promoting co-existence).
Whereas in a context in which the Krogan are being sought after as a military ally, the Krogan could be either the last remnant army of the genophaged race, all females dead and looking for a last battle, or a currently introspective empire in the distance. The prospect of the genophage-less Krogan empire concerns the galaxy, whether the Krogan are internally focused on cultural development (Wrex) or building their strength for conquest (Wreave). Regardless of the three outcomes, Tuchanka is distant and offscreen and the Krogan only serve a token army role.
And so on. Picking an ending scenario would let you address the main trilogy choices without letting those choices dominate the new plot. Even after a couple of centuries, the Quarian population is going to be small- no reason they need to be a cornerstone species of the next epic.
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