To be fair, I don't think peoples issues with the Destroy option were that they believed the Crucible - I certainly didn't, and no-one I know did. It was clearly talking gibberish hogwash because it's a broken genocidal AI. People disliked destroy because of the death of EDI and the Geth - a *totally* unnecessary FU to players to try and make the ending more of a choice than it was.
Partly that's because of the clusterfuck that is the ending overall though. Rather than stick to the genre, they tried a massive tonal shift in the last 15 minutes (Star Wars to 2001) and it utterly failed. Instead of destroy being the easiest ending to unlock, and synthesis the hardest, it should have gone:
Easy option: Control. You're losing badly against the reapers, life is facing extinction. You make it to the crucible, and in a desperate race for time your only option is to take over the machines and stop the slaughter. The galaxy is saved, but you have an ancient fleet of god like power still around under the control of Shepherd who becomes more and more isolated from humanity.
Middle option: Synthesis. With greater force behind you, you carve out enough time for a full assault against the reapers and take the crucible. Using the technology in there, you alter the reapers on a galactic scale so they understand organic life, bringing some of the chaos and uncertainty that organic life brings to their systems. The galaxy is saved, but the Reapers remain an existant threat - no longer united, but each still capable of destroying worlds.
Best option: Destroy, a.k.a. "Get the hell out of our galaxy". By doing something that has never happened before, and building on the knowledge and legacy of the Protheans, you unite all the races of the galaxy. Working together as one on a galactic scale, you fight the reapers to a temporary standstill, and then assault the crucible. With the force of a dozen major species, and ships from every race in known space behind you, you uncover the key to ending the Reaper threat once and for all. The reapers are destroyed and the galaxy can, for the first time in 2 million years, forge its own future free of the technology and interference from ancient gods.
(Could swap control and synthesis round actually. Synthesis I struggle with because the option presented in game remains, to me, the most morally appalling choice out of all of them and I just cannot see any possibility of *any* Shepherd, Paragon or renegade, choosing to alter the basic building blocks of life at a fundamental level for every single living thing in the galaxy without their permission),