Well that is the issue when people point out that Geth and EDI are ok with organics. Ignoring for the fact EDI is a singular AI rather then the Geth which are far close to the kind of set ups that caused problems in the past.
But EDI IS ok with organics, she even says that. 
The Geth are a different story and Shepard's actions will define if they are ok or not with us.
A playthrough of ME3 with Legion alive and trusted provides different information than a playthrough with a Legion-copy.
With a trusted Legion that returned alive from the SM, he explicit says the Geth do not wish to enter in conflict with organics because their experience when battling their creators and from what the geth collective learned from Legion's time with Shepard.
It also changes the perspective of the geth about the quarians, their creators.
Since the quarians were sucessfull in their attack to the collective, the geth intelligence dimmed and they only saw an exit by allying with the reapers.
Freeing themselves from reaper control, the geth act very different, accepting to coexist and cooperate with the quarians after gaining their intelligence back.
On the other hand if Legion is dead and replaced by a geth copy, the information he passes by is also very different, since he didn't returned alive from the SM and couldn't pass the information to the rest of them, resulting in the geth being alienated and with pre-conceptions of us organics.
This will result in the geth not trusting organics and only with the extermination of the quarians willing to do so in the future.
I'm not especulating, I'm simply using the information the game provided.
The main problem is: these two scenarios will result in several different outcomes and I can't argue with the Catalyst about them.
I can't tell to him the Geth (synthetics) learned about cooperation and symbiosis with organics, so he's wrong with his assessment about synthetics or agree with him that he's right and organics and synthetics will never get along.
I only have the option to acccept what he says... and that's it.
This also happens AGAIN when confronting Leviathan, I don't have a option to tell him to play high and go f**k himself, I only have the option to listen him talk about a bunch of nonsense.
If they are so powerfull and almighty and destroy a Sovereign class reaper in seconds, how the hell they let the AI conquer them? Because they had nothing better to do? Better yet, it wasn't even the reapers at that point, it was the thralls they claim to control.
Because, you know, they controlled the entire galaxy but didn't knew what was happening in that galaxy?
Oh look, we are being annihilated, but we can destroy those pesky AI in seconds with a burst of EMP.
Let's do this? Of course not, it's more fun this way. 
And if you are pratically a GOD and a organic mastermind, you want to prevent wars that derive from organics creating synthetics by constructing... a synthetic AI?
Wait a second! Then in reality this means we deserve the Reapers and being transformed in mindless husks and being used as "pasta al limone" by them.
So the endings are still flawed. 