A few points -
I'm not trying to debunk EVERY plot hole - just the ones that have popped up and that others have called "plot holes" even though they are clearly not. Either because they do not fit the definition or because they are actually explained quite adequately.
To address a few points raised:
A "rebellion" does not mean an unjustified revolt. I am well aware the Quarians shot first. That's why I let them die in my run-through.

That doesn't mean that they still didn't rebel. The Catalyst didn't seem to make any judgements about the synthetics, to me, when he said they'd wipe organics out. He didn't say it was unjustified every time. I just think the synthetics end up having the odds stacked in their favor.
Whether you agree with the Catalyst or not doesn't affect the basic logic of what he is saying. From his perspective and the long view he is able to take of events, his logic is sound. It might be horrific or wrong to you, or make you feel like you've ended up with a lousy set of choices. But people keep saying it isn't logical or doesn't make sense. That's not true. And since none of us have lived through millions of years witnessing the rise and fall of civilizations, we can't really say whether it's true or not. The Geth and EDI prove that not all synthetics are evil. That's why you're given a choice of destroying or not destroying them or joining with them.
But I don't think it's about good or evil. It's about two opposing forces, one of which becomes so strong it knocks every thing out of balance.
Destroying synthetics does not prevent them from being developed by organics again in the future.