Easiest way to stay in the Milky Way and NOT set a canon ending for ME3 is to bypass it all together.
In ME1, Kaiden mentions the 'Goose Chase' FTL tests the Alliance was running. So, who is to say those tests were completely abandoned. Now, an in lore explanation for FTL other than eezo can be used but only for propulsion, not for all the other uses. (true, the relays were a big part of ME but everything else still uses it so the concept is safe)
Now, the MW is huge and the relays are sparsely peppered through it. Move any ship, any person, 400 lightyears away from a relay and you have 400 years of playing around IN the MW before the (bogus) ME3 wave can hit you. With no active Relays around, the farther away you are, the longer the new 'series' of ME games can be used.
Not that I believe BW would ever do something like this but I just put this out there to show how a game could be done in the MW without worry of the ME3 endings.
Shutting up now. Have fun all. 