Well guess there's only 2 ways the story could progress with regards to the milky way, it's either:
1) Bioware already mentioned that they wanted to make MEA separate from the trilogy, if they hold true to their intentions, then the Quarian Ark would probably be the last thing from the milky way that we will see. Anything after that Bioware will need to commit to a canon ME ending.
2) Bioware needs to bring back Milky way elements for whatever reasons(needing to boost sales? needing to damage control and recover from poorer MEA ratings?), then they will need to sort out a canon ending for the ME trilogy(there are a total of 10 possible endings for ME3, redx3 outcomes(depending on war assets), bluex3outcomes and greenx3outcomes+ shooting the catalyst(cycle continues). Then possibly one of the ways they can do this is the ark as mass relays theory, Quantum Entanglement etc.