[Again, huge spoilers, obviously.]
I’ve been mulling over it since I finished the game, and I have to say that I think I like the ending where Shepard chooses to control the Reapers the best. Commenter xmenxpert disagrees, favoring the “Destroy” ending. I can definitely understand why one would feel that way; indeed, I had been planning to destroy the Reapers, but the final talk with the Catalyst changed my mind.
Let me explain how I arrived at my ending. For all of ME 2, my Shepard was pretty loyal to the Illusive Man, since he did save his life and no one else seemed to take the Reaper issue seriously. I preserved the Collector base at the end, because I figured having it gave us options, whereas destroying it was irreversible. I liked it the idea of controlling the Reapers and their technology for humanity’s benefit. To quote another BioWare game: “What greater weapon is there than to turn an enemy to your cause?”
I was planning to go along with whatever the Illusive Man wanted to do in ME 3, right up until the scene on Thessia when the Prothean V.I. states that at the end of the last Reaper cycle, the Protheans’ efforts to thwart the harvest were ruined by a rogue group that wanted to control, not destroy the Reapers. Later, it turned out that the Protheans in this group had been indoctrinated by the Reapers to sabotage their efforts.
This meant that Cerberus was nothing new, and siding with them would be playing right into the Reaper’s plans, and would cause the cycle to continue. So, I reconsidered, and resolved not to do what Cerberus wanted after all.
This was my plan right up to the last scene when Shepard meets the Catalyst, at which point the following exchange takes place:
Catalyst: Or do you think you can control us?
Shepard: Huh… so the Illusive Man was right after all.
Catalyst: Yes, but he could never have taken control, because we already controlled him.
Control of the Reapers was possible, the Illusive Man had just screwed it up. But Shepard hadn’t made the same mistakes, and so he could take control. I think this was the significance of the blue (Paragon) color being used for the control ending and red (Renegade) being used for the destroy ending. It was a plot twist of sorts: the Illusive Man had wanted to do the right thing, but out of evil motivations, and Anderson had wanted the wrong thing, but out of pure motivations. So I chose Control.
Now, you may object that this decision rests solely on trusting that the Catalyst is telling the truth, which is a gigantic leap of faith given that (a) you just met it 5 minutes before, (b) most of what it says to explain the choice is vague nonsense, and (c) its original plan and reason for creating the Reapers is a patchwork solution at best and utterly insane at worst.
All of these are valid objections, and in a really good ending, you wouldn‘t have to trust the Catalyst. But, with the choices the game gives you, you have to take Its word for it or else let the cycle continue. Consequently, I would argue that the Control ending is the best of the available choices.