Since 3DandBeyond hasn't replied to Holger's latest, I'll take a small crack at one part of it.
Holger says that there's no evidence that the Crucible is a Reaper Trap. True. But there isstill the possibility, even the liklihood of it. Javik and the Prothean VI both say that the Crucible is cycles and cycles older than they all thought it was; that every cycle adds to and improves on it.
To me, this introduced the STRONG possibility that the Reapers had created the plans, and at least used it as a Red Herring to keep the organic peoples attention while they were Reaped. When we find out in the end that "The Crucible has added new possibilities" as Starboy says, I immediately thought that this was all part of their plan. I figured that the Reapers, or Starboy himself, had theorized that through the crucible they could, I don't know, do something that they wanted. The Synthesis Option is positive for the Reapers. The Control Option puts us in a situation where Reapers survive and there's a body-less consciousness controlling the reapers; exactly what we have when Shepard encounters Starboy. And the Destroy Option kills the reapers, but ALSO kills your Synthetic allies. Synthesis seems like the "best" option when you discount the horrible horrible injustice done to people when you pick it.
I have to wonder, are we SURE that nobody ever completed the Crucible before? Javik said no, but he didn't know about Ilos. He was a soldier, some kind of officer, but would he know if the Crucible was completed or not? I don't think so. Maybe they provided the Crucible just waiting for some cycle to come along where someone would pick Synthesis. Maybe they need a willing merger, forcing it just results in abominations.
Consider what the Reapers do when they learn that we've built the Crucible: They take the Citadel, which is the CATALYST, to Earth. Our Homeworld. Which we have just assembled a SUPERFLEET to retake. Then they build a Conduit to it. A conduit that goes not just to the Citadel, but to a hallway that's about, let's say, 200 yards from the Catalyst/Crucible control room. When the Crucible is attached to the Citadel, the arms are WIDE open. The Arms are held on by tiny little structures. The Crucible's armor has come off. It's docked on that flimsy little ring there. The Crucible is the ULTIMATE WEAPON, right? It can destroy the Reapers, RIGHT?!?!
Not even ONE Reaper seems interested in this. None of them take a shot at it. They don't send any banshees or brutes or harvesters or cannibals or even husks into the Conduit after Shepard.
Shepard walks past at least 2 Keepers in the charnel hallway; they ignore him. The Keepers are Reaper Pawns, we know that from the first game's lore.
Before Shepard even gets to the hallway, Harbinger is firing his Reaper Beam RIGHT TOWARD HIM. But Shepard survives. What? A smaller Destroyer class reaper hit an armored Alliance shuttle with that beam for half a second: the shuttle popped and everyone inside was so much ash. It hit a second shuttle a second later, BANG, same result. But Shepard's A-OK after his run-in with the Harbinger Beam. Oh, and then Harbinger goes away. As Shepard's clearly getting up, on the way again. His hair's still there, BTW. My armor was seared and melted, and I wasn't wearing a visor. But my hair hasn't been burned to a crisp. Okay, that's not valid, they can't account for hairstyles, but still.
Personally, I feel like that entire last scene there was designed to make Shepard THINK that he'd won. To make us think that we'd won. Except we all feel like we lost. But really, think about it.