Okay so at the end of the game they tease that a Quarian ark has sent out a warning saying that people should stay away.

This could mean several things.

- Since its a warning signal, I doubt it means they are under attack by the Kett. Otherwise such a beacon would draw the Kett to them. This possibly means that the Ark has either been captured by the Kett or has been left unsafe because of the Scourge and the Quarians have left for a planet instead. A third alternative is that they're worried the rest of the Adromeda Inititative will discover what they are up to, but this again makes little sense because they would be alerting the rest of the Initiative and the Kett.

- Now, a general recurring theme of all the entire initiative is that everything that can go wrong has gone wrong from the Scourge to the Kett to the planets themselves. The Quarians would have ENORMOUS problems dealing with these things due to their fragile physical forms and weak immune systems. Its also repeatedly stated that the Quarians aren't useful in a fight as any small puncture can cause a nasty sickness that leaves the warrior useless. Plus if they have had to abandon their Ark and settle on a hostile world then all of these problems would be magnified ten fold.

- We also see with SAM that they want to push the idea of AI and humans working together in a symbiotic relationship. If you get the Quarians and Geth to work alongside eachother in ME3 Tali even suggests that something very similar is occurring with this helping to heal the Quarians and allow them to live on Rannoch. Plus with the Krogan genophage they avoid repeating the past conflict by arguing that they evolved something of an immunity. So clearly Bioware wants to nod to these issues being settled in ME3.

- This means I am pretty convinced that the Quarians, when they fight the Kett and have to settle a world will build new Geth to help and protect them. However, because they're part of the Andromeda Initiative and so presumably more open minded (as they have given up taking back Rannoch and left the Migrant Fleet); so they actually form a symbiotic relationship with the Geth. Basically it will be a "what if the Quarians hadn't been stupid and tried to exterminate their loyal Geth servants". Legion made it clear that both species could live together if the Quarians just accepted that. Circumstances being as they are, I can't see the Quarians not doing this and it would allow both races to be incorporated into the Nexus.

- Building lots of Geth will enable the Quarian Ark to fight the Kett and they can use more Geth esque implants to improve their physiology similar to what the Pathfinder does; possibly even linking in to the Geth network. If the Quarian Ark has a SAM and a Pathfinder it could be that having an AI to act as an intermediary helps facilitate this. I mean I can't see any better way of pushing the whole Organic/AI symbiotic relationship thing than using those two species to do it.

- It would also pave the way for us getting a Quarian/Geth companion.

As a sidenote: I think it would be really cool if by some random accident (wormhole?) the Quarian Ark arrived a few decades before the rest and so had time to fully settle and build this Geth/Quarian society. Maybe it reaches the point where the line between Quarians and Geth starts to get blurred and goes full trans-humanism? It would be a great way for them to explore things that were brought up at the end of ME3 between the Quarians/Geth but that they were never able to explore further.

Personally I wouldn't want them to make more Geth and then the Geth betray us/Quarians try to kill them. That has been done and I would rather see them both supporting eachother.