I didn't mind Miranda's devotion to her sister and all that. I thought that was the greater focus, rather than her daddy issues, because to me, that seemed more important to her because she didn't share it until Oriana is in trouble. The daddy issues seemed superficial, but once you get closer to her, you find out about her sister.
I wouldn't mind seeing more sibling relationships as opposed to parental issues. But the thing is that parental issues are present in many people's lives, but I would want a greater focus on blood-family. Maybe a crew member could be Ryder's sibling or sth, and that leads you to making a tough choice.
Organics vs. Synthetics is quite inevitable I think, although I do not think it will be as strong as organics vs. Reapers.
Zombies. If they do zombie or undead type stuff again, they have to be really careful. I felt the Thorian creepers were way to similar to husks in ME1. And there's also all the indoctrination stuff which is so Milky Way right now. So they should probably avoid it. They can still do diseases, or plagues (maybe one hitting a colony or the ark) but no walking dead pls. There are other ways to creep us out.
References or themes from Mythology are fine, I guess. Lazarus, Space Jesus, The Shepard are quite strong, and they should only be subtle underthemes next time I think.
Also, this is not really intentional and is more a design thing, the technology and atmosphere changing vastly game to game. If they do a continuation of ME:A, I want the level of technology and architectural design to feel the same, and have a similar feel. It's not like technology just jumped 10 years between ME1 and ME2. I hope they can keep a consistency in that sense, unless the design turns out to be **** in ME:A, but as I said, that is not intentional