1. Why did the Reapers stop at the Milky way galaxy? Let's say they had managed to wipe out the galaxy, would they have stopped there or continued on to other galaxies to wipe them out? Would they have eventually arrived at Andromeda? If not, why didn't everyone just pack up the moment the reaper invasion was known to be a guarantee and head to a new galaxy and start anew?
2. Why is the main guy still flying the N7 colors? Are the Systems Alliance Military on Andromeda? Since this is a new galaxy shouldn't the governing unit be something other than the Systems Alliance?
1. According to Vigil, the reapers would normally enter the Milky Way via the Citadel Mass Relay. I've theorized that the Citadel may operate similar to a Borg Transwarp hub and this is possibly how we get to Andromeda. In this case, regardless of how shiny things are back on Earth, there will always be a human drive to expand and colonize further than before. In my opinion, we're picking up the Mass Effect Universe just as Citadel races expand into a new frontier. (Have you seen how fast Krogan can pop them out?)
2. I'm assuming the protaginist N7 will basically be playing the role of Nihilus. In Andromeda, your character may be asked to join the N7 depending on (I'm theorizing here) what background you pick. Some players have mentioned that they wished the could have joined cerberus, or been a straight up mercenary, so I'm somewhat hopeful you can get some choice to start with the Alliance, as a Mercenary, or private military group.
Since the N7 is a vocational code of the Alliance Military, I'm assuming they will have some influence in a military role, although we don;t know how large that will be. The Systems Alliance is the governing body for Human planets and colonies and military. I don't see the need to change it from a lore perspective. I figure Andromeda is just political posturing by colonizing new worlds.