First, just how did the Reapers manage to reach our galaxy without the Citadel Relay?

Answer: they had to heavily modify their corresponding Dark Space Relay to serve as a slingshot of sorts, flinging them towards the edge of the galaxy as we saw in the Arrival DLC. Doing this required massive amounts of Element Zero, meaning they actually had to sacrifice many Reapers, or at least reduce them to minimal functioning, in order to get that much eezo. Which leads to...

What exactly was the big deal about Dark Energy? ME2 made it seem like that was going to be an important plot element.

Answer: it is necessary to the creation of more eezo. If I remember the codex correctly, eezo is created when a planet or asteroid is subjected to the energy of a supernova. Hence the experimentation on Haestrom's sun; the Reapers wanted to artificially create supernovas so that they could replenish their own eezo reserves (and maybe to save their brethren floating around in Dark Space) while making sure that there would still be enough for future organic races to discover and be able to use Mass Effect technology, thus allowing the cycle to continue.

Third, near the end game the Reapers took the Citadel to Earth? The frak??? I mean, really? Between the time it took Shepard to leave the Citadel and go to Cerberus HQ, the Reapers (who have been moving as slow as molasses) manage to arrive at the Citadel, wipe out every last trace of life there, AND tow it to Earth. Wow. That's really what we're riding with???

Answer: no, the Reapers did not move the Citadel, it moved itself. "The frak? How does that make any more sense?" Creepy Citadel Force Ghost Child, (who the Protheans had inadvertently taken out of commission back when they altered the signal to the Keepers) is awakened because the Citadel is able to detect the energy signal of the just-completed Crucible. Instinctively, it transports the Citadel to the largest concentration of Reapers in the galaxy, Earth, to try to protect the cycle. As for how this happens, well it is the Citadel, there is still a great deal that people don't know about it. Is it really that farfetched that it has its own means of propulsion and/or FTL?

Why do the Reapers care about the cycle?

Answer: the cycle is pretty much what was stated in ME3, an attempt to preserve organic life before it could wipe itself out with its own synthetic creations. They truly believe what they are doing is not evil, just a necessary part of preserving the natural order of life. Of course that reasoning is flawed as hell. Shockingly, melting organics into a paste and then using said paste to create Reapers is not the best way to preserve a species. They are, in fact, perpetuating the very thing they were supposed to prevent. They just can't grasp that concept because they can't fully comprehend what it truly is to be organic. They need a Catalyst.

What is the Catalyst?

Answer: someone who can truly bridge the gap between organic and synthetic. Was never crazy about Creepy Citadel Force Ghost Child being the Catalyst because, if it was that damn powerful and knew what was going on, why even bother with needing the Keepers to run the Citadel to begin with? Better that it just be construct of some long-dead race, tasked with finding a solution to that "technological singularity" thing. A person, in this case Shepard, someone who combines synthetic and organic tissues, can bridge this gap and bring true understanding to the Reapers.

Even though I liked the "synthesis" ending the best out of the three, I would do away with it. I already saw the ending where the descendants of survivors from a doomed civilization are actually organic/synthetic hybrids, it was called Battlestar Galactica. That's not to say I would totally scrap all the cinematics, the shot of Shepard falling through that green beam was much more powerful than just shooting a glass cylinder or grabbing some metal rods.

The basic end choices would be destroy all synthetics or control the Reapers, the color of the beam depends on your choice (red for destruction, blue for control). The exact endings would be based on certain criteria-

Worst endings, bare minimum Effective Military Strength: very similar to what's already in the game. The energy of the Crucible destroys the Mass Relays and their star systems, leaving only a small number of survivors stranded on remote planets, cut off from each other. Though there is some hope that someday they can rebuild and discover new methods of FTL, the reality is that organics have paid a very dear cost to defeat the Reapers.

Moderate endings, moderate EMS: Shepard still dies. Crucible energy burns out the Relays, leaving them inert but sparing their star systems. At least civilizations survive, yet without the Relays they will struggle mightily to rebuild and recover. A Dragon Age 1 style slideshow will inform the gamers of the ramifications of their choices throughout the series.

Good endings, high EMS: same as above, except the Relays are not burnt out. Though the Reaper War was devastating, inspired by Shepard's example the races come together to rebuild and enter a new dawn of civilization... at least for a while. Again with the slideshow to show the long term impact of Shepard's choices.

And for the romantic in me- best endings, EMS equal or greater than above, Garrus survived ME2, insanity difficulty only: same as above, except Garrus (who has some cybernetic implants himself) sacrifices himself in Shepard's place, allowing Shepard to continue to lead as all the races work to rebuild. Similar to DA1 if the Warden survived, Shepard can actually speak to the survivors and really bring closure to many of their storylines. Throw in some happiness for the love interests (lots of little blue babies with Liara, poetry with Ash, boring crap with Kaidan, whatever), or some private reflection of the LI is dead (Garrus, Thane, or if the LI died in ME2).