I'll admit I have a very limited understanding of astrophysics and am appealing to better minds for their input on the validity of this suggestion. 
One thing I found appealing in Mass Effect was the way Bioware handled the Fermi Paradox with the Reaper's cycle acting as a great Filter mechanism throughout the history of the Milky Way. It was a cute idea at first, but I believe it also had inherent problems from a story perspective because of the sheer difference in Kardashevian scale levels between the cycle species and the Reapers made conflict impossible to achieve without the serendipitous discovery of the Crucible plans at the 11th hour of the last cycle
My hope is that Bioware do not choose to create another Apex type civilization in Andromeda and that they keep any antagonist species at a relatively equal Kardashevian scale level as the MW species that crossover. To make this logical though would require another Great Filter/Great Silence mechanism that operated within the timeline of the Andromeda galaxy that would cause mass extinction events and reset the clock on Civilization.
I found this article on Andromeda that states that Andromeda has a far more violent past than the MW and that it has been more cannibalistic of smaller galaxies than the MW in the recent past.
http://www.dailygala...-milky-way.html
It may be my limited understanding of the physics, but I don't imagine that colliding galaxies are benign environments and believe that they possibly could operate as a combined Great Filter/Great Silence type mechanism that justifies the Fermi Paradox and keeps the species at a relatively equal level on the Kardashevian scale.
Anyone have any thoughts on this?