User blog comment:The Milkman/No Love For Leviathan?/@comment-24174486-20120915231103/@comment-24174486-20120916185313

"Right, but the Normandy still crashes in Control, didn't you think that was odd?"

The mass relays aren't destroyed in Control, but they still are damaged.

"The climax and resolution of the story is supposed to wrap up the conflict, not introduce a new one."

"Commander Shepard, it is up to you to decide the fate of the Council. Is the sacrifice of human lives a price that needs to be paid, or should the Council be abandoned?"

"Shepard, the Illusive Man wants you to preserve the base by poking this deus-ex-machina terminal. But you can choose to destroy the base using the same terminal.  What shall you do?"

As for ME3, it does not add a new conflict but a new view on your options for resolving the main conflict of the story.

"The energy of the Crucible now allows these options: Destroy – sacrifice the unsuccessful solution and remove the current roots of the organics x synthetics conflict"

There's nothing to suggest that Destroy will destroy synthetics simply because the Catalyst wants it to. The fact that it destroys synthetics as well is the reason why it views Destroy as a poor choice.