I think ME3 would have been better served with more examples of AIs still wishing to stay as separate AIs instead of 'more human/organic'.
As it is, it seemed forced without counterexamples. I didn't see as many organics trying to be like synthetics. Why do I have to keep seeing every synthetic in ME3 trying, at some point, to be more like organics?
I get that synthetics can have a different mindset when networked and go with the crowd of programs more (if enough Geth want to change, pretty much all of them will do it), but still.
I'm fine with some synthetics wanting to be more organic though. I'm fine with organics wanting to be more synthetic. Cool. That move in the story was something I even anticipated to a degree. But ME3 seemed to push it more than I thought it should. There still should have been AI that even by the end, never develops any interest in even interaction with organics.
ME3 may have a lot of the Blue around, sure, but when it came to the synthetic life thing, so much seemed to be more about the Green or Red. No choice to go 'Hey, you synthetics be you, and we organics be we, and we be good, yes?"
I do think that should have been one of the ways to go. Instead, we're told that organics and synthetics cannot do their own thing at all, because:
-synthetics will be used as tools if they are still separate from organics, or else they are destroyed by them, or retaliate by destroying organics
-organics will integrate more synthetics into themselves so a merge will happen at some point anyway
-synthetics will become more organic-ish at some point anyway
Well I personally don't see that as utterly inevitable. And I would have liked to see examples that allowed this concept, like ME2 did.
Even Control went 'okay synthetics can be separate and do their own thing, even in peace with organics, but it requires a Shepard entity aka an organic-ish thought pattern to guide it'. No. I think synthetics can do this on their own, with our cooperation.
Again with the 'integration' agenda. One I actually support in some ways over separation. But I don't want to feel 'forced' into it 
This is partially why I switched from Synthesis to Destroy. Control wasn't an option I could support. Synthesis fit some of my ideals, but not in the way I wanted it to.
If there was an actual option to, say, hand the reigns of the Reapers over to a committed-to-peace Geth (may require a differently written Rannoch arc), I might have gone for it. At least synthetics would still do their own thing, but just in cooperation and thankfulness towards organics and Shepard. It would carry its appropriate form of risk (Blue always has that though), but if I already made 'friends' with Geth, that shouldn't have been a problem.