Oh I get why they were destroyed, I just don't get how.

Likely the same ray that has spread through the mass effect relays and fried pretty much everything with a hint of technology in it's path, including the Normandy, what I found DAFUQ was the fact that Normandy was fleeing from the battle? And Garrus was on board? He was just only rushing tower with me, unless about a few days passed since when you get beamed inside, it just doesn't make that much sense. What I find annoying as hell though is, no matter which scenario you pick, mass effect relays are gone, methinks Bioware are looking for an easy way out should they proceed with this franchise, as the world they'll create will likely not need to be as big due to lack of fast transportation.

Actually, if the endings are indeed events happening and not some indoctrination/hallucination attempt (I still really, really doubt that what we have seen is the real deal, since they clearly show shepard to be alive at the end of the Destroy ending in the midst of concrete rubble, which can only be after Harbinger's laser nearly hitting him), there's an explanation for why that energy beam destroyed both the Geth and EDI along with the reapers.

If you read carefully through the War Assets and compiling what the Protean VI says to you in the Cerberus Base, the Crucible is just a massive Dark Energy generator which the Citadel then concentrates and sends out to the entire galaxy using the relays. Now, what do the relays, the citadel and every advanced synthetic in the galaxy have in common? They're all based on Quantum technology (either for shielding, processing power and/or overall structure). So it could be that the Dark Energy burst destroys anything that's based on Quantum technology (that would have to include the QEC's as well as some of Shepard's synthetic prostetics. 

Of course, I can be wrong, but that's what I recall from the lore. Anyway, I still get the feeling any theory we can come up for what were those energy rays is pointless, since we'll end up getting a more detailed ending scenario in the future.

Admit it guys, it was simply a bunch of FTL pixie dust that stands far from the codex explanations that made ME (almost, if you wish) hard sci-fi.

No need to play the apologist for Bioware or beat even further a dead horse. It is as it is.

It was given an explanation. A very poorly done and frankly lacking explanation, but it was given. Still not convinced that we have seen all that there's to see from ME3 final moments, especially since the events of Arrival were the true final moments to ME2 instead of just the Collector's Base destruction/purge.

Everything is' based on' quantum technology.  Quantum technology just exploits quantum effects present at the subatomic level of all particles, the same particles we and everything around us is made out of. You can't say something selectively destroys quantum technology.

Hey, I never said what I thought was a perfect explanation

As for quantic matter states, it's true that at sub-atomic levels it's present, but at very defined states. You cannot overlap quantum technology with what it's present in observable nature, because the quanta of matter are in defined and observable states. As I recall, quantum theories for computation deal with all possible states being overlapped and analyzed by a single qubit, which is something that doesn't happen naturally in matter, as all matter is observable thus it's "locked" to defined states. Schrodinger's theory is only appliable at Wave levels in matter, and even then in a very restrictive parameter set.

Theres going to be DLC to fix/extend after the ending. I think It's obvious when they even say there will be DLC after you beat the game, not to mention the amount of pissed off people once the game was done.

Probably my favorite game on the 360 if they can offer enjoyable DLC (right now It's Mass Effect 2, followed by Bioshock).

Exactly, you said it yourself - the explanation lacks explanation.

Frankly, the only way they  they could get away with the crucible was making it somehow harness the staggering energy of the mass relays to shoot deathstar rays at the Reapers, and destroy the relays in the process if you please, that would explain why the reapers don't make use of such a weapon. Or maybe a different type of FTL drive who doesn't shut off nearing a collision, so all the allied ships just kamikaze on the Reapers. It is said in the codex that it would work, so... and even if someone designs a way to explain the red pixie dust, we'd still have a control who doesn't make any sense at all - Godkid controls the reapers, why he needs blue pixie dust and disintegrate Shepard to call them off?  - and the synthesis thing that is just atrocious and full of unfortunate implications. 

Yeah, the Control and Synthesis endings are far too poorly done to be accurately explained by anything ever said in the lore of the games. Frankly, the only scenario which is slightly plausible is the Destroy one, which as oddly as it seems, by believing the endings to be actual ocurrences is a renegade or bad ending, which kinda seemed "off" to me (well, that and that shepard awakens in the midst of rubble afterwards, but there's no way him or anyone could have survived to destruction of the Citadel)