Fate of Ellen Ryder

My admittedly lame 'theory' is that they're keeping the mother a secret, so as to make room for the possibility that the twins can be customizable w/ respect to skin color etc. while remaining the biological offspring of papa Ryder.

E.g., my Ryder will be black; so in order for him to be Alec's biological son, the mother would need to be black as well. Being the biological offspring could be significant in some way.

Well they could do what the did with Dragon Age 2 and have several presets for parents/siblings to account for player creations.

Her getting killed during one of the events from ME1/ME2 is definitely a strong possibility. The way the devs have mentioned the "Ryder family mystery" makes me wonder if there's something deeper.

Other thoughts:
-She was indoctrinated.
-She was imprisoned for life for illegal work on an AI.
-They got divorced, now it's awkward.
-Died at childbirth.
-Disappeared in dark space. Some kind of plot bunny convinces Dad!Ryder that she ended up in Andromeda. Mystery ensues.
-Mom!Ryder made come kind of crazy discovery about Andromeda, then died under suspicious circumstances before she could reveal it.
-No one ever helps her with the dishes in this god damn house.

It was confirmed that he isn't customizeable, but will change appearance based on siblings.

There goes my lame theory.
I suppose the twin's appearance also changes accordingly.

No, the briefing only says Alec became interested in AI at the end of it's description, which imply he started building SAM probably a few years before the initiative launch. He probably became interested in AI after coming back from the Charon's Mass Relay, which opened new frontiers to the humankind. His wife must be helping him until something happens..

Tell me more about this plot bunny...

Hopefully she'll appear at some point, or maybe Alec has her audio logs that we'll be able to listen to. Voiced by Sigourney Weaver. For reasons.

 Quiet! Make it stop!

SAM = Ellen Ryder. That was kept a secret. Ellen Ryder didn't just help develop SAM, she is SAM. Aided by the illusive man and project overlord technology. She could have been dying from a degenerative condition.

SAM also stands for Scott/Saras Actual Mother.

In payment, Cora Harper, the illusive mans daughter, was given a prominent position on the expedition, as Alec Ryders second in command, to further humanities interests in the helios cluster.

She was born in London, then either died on Eden prime or was one of the scientists that we saved. Or she decided to stay in the Milky Way for one reason or another.