Didn't the Andromeda mission launch before the end of ME3? A contingency plan, in case the Reapers won, for humanity to survive elsewhere? If that's the case, I don't see why they need to address the novels at all. Ryder's voyage took hundreds of years to Andromeda. Nothing that happens in the Milky Way should affect this mission when they're so far away.
On the morality system - I agree with much of what has been said. What I'll add is that it affected my playstyle in a way that made it very boring. I became very passive in dialogues. Instead of looking at the options displayed and seeing actual words, and thinking about those words, about how they'll affect the character in front of me, I just saw colors, and height. Blue on the top, red at the bottom. It became an automatic, thoughtless process that rarely challenged me at all. I'm glad it'll be gone, and I also hope there won't be any icons to signal if this dialogue option means this or that emotion. This should be obvious from the words themselves. Reducing it to signs and location on a wheel is just one step further removed from player thought and activeness.