There was no option for a story of the scale we saw in ME 1-3, if it would happen in Milky Way.
Reapers were the biggest threat - continuing the story arc of Milky Way would require involving the player with only some conflict between races, corporations or institutions - which would be really underwhelming, when you consider that in previous games you fought 2 km long superdreadnoughts of incomprehensible intelligence, trying to harvest all life, which were several million years old.
After Mass Effect 3 there are hardly any secrets in this galaxy worth knowing. Everything was controlled by the Reapers anyway, and they are either gone, or working for organics (or everyone is a green, organo-synthetic being, including the Reapers).
Rebooting the series and finding a new galaxy, with new secrets, new races and new lore was the only way to go if they were to continue the franchise.