Mass Effect 3 Plot Holes (Explanation?)

[Seanfall]

Even the leaked dark energy ending feels kind of meh to me. Sure the dilemna's a bit better, but it still has the problem of the last-minute "we're not really the bad guys!" ass-pull.

same here...I mean they where so much more menacing when we had no idea why they did this. They where unknowable gave nothing about themselves away, and saw us Shepard their greatest foe...as a minor annoyance. That was good. The Dark Energy thing at least makes an amount (though small) of sense. The reason we got...doesn't.

 

[SajuukKhar]

The "Synthesis" ending seemed like it tore open another giant plot hole. If the Catalyst could fuse organics and synthetics in order to keep them from killing each other, why not do that in the first place?! Why bother with the Reapers at all if you've already got a full-proof, peaceful solution that doesn't involve slaughtering trillions?

Sure, you need a high war-readiness and presumable the Crucible has to be really well-built to pull it off, but if you've got the capacity to build Reapers in the first place, whipping up a Synthesis-quality Crucible shouldn't be a problem.

He specifically said the crucible gave him new options.

He COULDN'T before the crucible was added.

He also stated he couldn't make the choice himself. Presumably doing anything but what he has been is outside his programming.