Can the Reapers be Removed From the Equation?

Let's see ... 600 years after ME3 ... give or take a year ... some folks arrive in Andromeda. The travelers and their descendants tool around Andromeda for a millennia or so. Someone decides ... hey, let's take another 600 year journey back to the Milky Way. So ... 2200 years or so after ME3, these folks arrive ... to what? Not anything that looks like ME3, regardless of canon. Which, maybe would be the point.

Refuse ... if the Reapers won, then the explorers would return to a MW galaxy that was very early in the 50K year cycle and they would most likely be the most advanced civilization in the MW ... assuming that the MW Asari, Humans, Krogan, Turian, Quarian, Batarian, Drell, Hanar, Elcor, Volus, Rachni and even the Vorcha are no more. That leaves what? The Yahg? So, do they find some of Liara's "beacons" to discover what happened ... and then, do they beat feet back to Andromeda or prepare for the Reapers in about 48K years? Would they know to destroy the Citadel or would they just modify it, so the Reapers couldn't use it and it would no longer start the cycle?

Destroy ... well, with 1200 years of development lost in the trips back and forth, the Andromeda folks would be the "primitives" in this story. Rebuilding in the MW would be required, yes ... but that would be done long before the ark ships arrived in Andromeda ... plus, Reaper tech to help advance things.  So with 1200 years lost to cryo-sleep, the Andromeda folks would be fairly far behind ... even with advances made from Andromeda species tech.

Synthesis ... hmmm ... wonder if the folks from Andromeda ... not being of the "synthesis" would be perceived as friend or foe ... maybe the synthesized folks in the MW would be like the Grey Wardens in DA:I ... once heroes, now corrupted foes.  Except, instead of the few, they are the many.  And perspective ... the Andromeda folks would be ... from the MW folks' perspective ... the bad guys.

Control ... instead of Harbinger, we now have Shepard. How does that play out? Does "Shepard" eventually harvest the organics? Become a benign god who rules over both synthetics and organics? How well would "Shepard" tolerate those who had not been enveloped into "the one true way?"

Regardless of canon, some interesting possibilities ... a lot of them seem to lean toward the old good guys becoming the new bad guys.  Such as a protagonist from the MW having to deal with the Andromeda invaders.  Maybe the protagonist choice isn't just male or female, but also MW or Andromeda origins.

If ME:A is a trilogy and it takes nearly a decade to grind through the three releases ... before starting the next ME trilogy ... will anyone care at that point, what the ME3 canon is? 

Well, yes ... some will care.  Some also travel to Graceland every year to worship Elvis ...