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Darc Requiem said:

4. People were pissed off at the plot holes. ME2's Arrival DLC established that an exploding Mass Relay has the force of Super Nova. No matter what ending you choose all the relays are destroyed. Which means nearly all life in the ME Galaxy should have been wiped out. The Normandy was with the combined Galactic Fleet above Earth and suddenly it's at FTL out running some explosion. One of, or in some cases both, squadmates you take into the final battle on Earth exit the Normandy's hatch after it crashes. That's not even possible. The Illusive Man controlling Shepard and Anderson was plot hole. Indoctrination has never worked that way throughout the entire series. The reason the Catalyst gave for creating the Reapers made no sense. To stop synthetics from wiping out organics, the Catalyst creates a fleet of synthetics that wipe out organics. The ending literally made no sense. It reminds me of the Mass Effect Deception debacle.

Not sure if we're still doing spoiler tags so I covered part of my post.

Just a comment on a few of the plot holes you mentioned:

1. Supernova's (whilst huge) aren't that big and there aren't that many mass relays. There would be plenty of life left after the destruction of all the mass relays.

2. The Normandy suddenly appearing in FTL with members of the crew (including those that were down on Earth) points to a gap in time that I think will probably be filled with the DLC. As it stands, it seems pretty random, although I'd guess it was trying to outrun a mass relay explosion... but yeah...

3. The reasoning the Catalyst gave was to prevent further chaos a complete and all out war would bring. My understanding was that in a 50,000 year cycle organics become too advanced and will lead to a completely chaotic situation whereby organics and synthetics battle continously for millenia. This is heavily hinted towards by the Geth and Javik's complete distrust of synthetic life.

The Reapers pupose is to massacre advanced organics, not battle them in war. Anyway, the fact that Shephard made it into that room in the Citadel showed the Catalyst that the organics of this cycle had advanced to a point where the Reapers were now redundant and wouldn't be able to prevent the chaos they were originally designed to.

This of course leaves more questions as to the nature of the Catalyst.