The Quarians seem far too sensitive, one of the reason they couldn't find a new homeworld was that they had trouble enduring the ardours of spacetravel and gettign too far away from civilisation that could provide them with needed medications and other things they needed.
Taking them with us to Andromeda Before the end of ME3 and a futore where the Geth fix the Quarians immunesystem... I don't see that happening.
If they want to avoid the endigns then they will launch some time before the ending to ME3.
If they launch after thessia, then there could be Geth and Quarians aboard if they are allied with the rest of the galaxy and the council.... Though the Quarians still seem quite fragile.
A Geth Quarian Peace, could probably be the best bet for the Quarians beign in, but I somehow doubt BW want's to force the decision. Unless they add a bunch of Quarian exiles, who had admirable reasons to being exiled and might have gained the Councils acceptance.
The Geth could have Legion faction Geth who are Legion Geth that are some kind of subgroup that's kind off broken off from the main Geth collective.
Somehow I have a feeling they might scrap both of them.
Still, they didn't scrap the Krogans and some pretty big decisions were available for them. No matter how huge the Council/Krogan divide could grow, we will still get Krogans in Andromeda.
So, I'm thinking they might try to include the old species we know, and add some new ones. Don't expect to get every species as a possible squadmate in ME:A though.
The Quarians and Geth are probably the hardest to include as a part of ME:A. If they want to avoid big decisions and the endings.
TBH, I would like to see both of those, not sure if BW can manage it though.... But if they can make Another game after ME3, then , I guess they can make anything happen.