BioWare can either:
A ) Canonize an ending and hope to build a satisfying sequel off that
B ) Actually go forward with IT (or steal it depending on your leanings on it) and make an actually satisfying conclusion for the series
C ) Decide the endings fucked up the galaxy so much, and were so wildly varied that they're just gonna give up and go to an entirely new galaxy
If you know me you know which option I'd prefer, but either A or B are good. If they go for C it will just be embarrassing.
I disagree.
Making an ending canon would invalidate too many peoples endings. I can't image anyone would end up happy about an ME ending being forced upon them.
Personally, I think the 'synthesis' has huge potential to make a really interesting future for the Milky Way Galaxy, but I know I'll never see it because it would mean BioWare would have to canonise an ending.
Canonsing an ending would've made all the games with save transfer easier and they have never done it, so I don't think they'll do it now.
As for IT, it is a fan theory, can you imagine the backlash BioWare would suffer if they stole a fan theory? The forums & twitter would explore.
I'm also sure that they began writing the story for NextEffect before ME3 was even finished, so their planned storyline would have to be changed completely to use IT.
I actually think the idea that the NextEffect takes place in another galaxy is an interesting way to allow players to keep their endings from ME3 & at the same time, not have to deal with them much.
Full Disclaimer though: I'm a huge Voyager Fan, so the idea of a ship full of people from the Milky Way exploring a new galaxy, with little to no contact with their home, really appeals to me.