Post of the thread, Aske.
Disclaimer: Opinion, etc.
The sad thing is the main counterargument to the Shep has disproven the catalyst's argument is that the catalyst has been around for much longer than Shepard and therefore should be taken at face value, given his/its relative all-knowing status over hundreds/thousands of cycles, while we as the player have only experienced one.
It's the ultimate example of "show, not tell" that Bioware (if that was indeed what they intended by not allowing the argument) got wrong. They either give solutions that aren't given any real level of thought into their consequences or feasibility beyond the "end the reaper threat" such as synthesis, give solutions that we have fought against all i.e. control, or are forced, arbitrarily in my opinion, to destroy a potential race of friends the geth to prevent a lot of people from saying those all suck except for destroy.
And either way, no matter what, Shepard dies and the relays blow up, and your ship mysteriously gets damaged and then stranded on a jungle world.
And if Shepard doesn't die in the destroy ending, as is hinted with a high enough EMS to somehow make the crucible 'better able to distinguish reaper tech' (that's the main theory I've seen), it invalidates the other two options as valued choices, since you can do the same thing, save the galaxy and the characters you care about, but have the added bonus of having Shepard live.
It's like the ME2 suicide mission. Once the best option becomes available, a lot of people will strive for that perfect ending. That ceases to become choice-based role-playing to a lot of people. Why strive for a shitty choice/ending when a better one is available, especially when it's available from both a Paragon and Renegade perspective.
Synthesis is given to us as a solve-everything magically scenario, and Control, what we've been fighting TIM on, provides no tangible benefit over Destroy, at least in terms of the universe other then MAYBE rebuilding the relays faster using reaper tech and the geth not dying, though Bioware has hinted that with a high EMS, the geth won't necessarily be destroyed either, further invalidating control as a serious choice.
Unless Synthesis or Control are given tangible differentiated rewards from destroy (which I doubt we'll really see, since Bioware is holding to their "your ending is based on how you imagine it") I can't see many people picking things other than destroy at the end of the Extended Cut from a role-playing perspective. To see what happens maybe, but with a choice-based RPG system, the player generally wants to be the hero who saves the day, rides into the sunset, etc.
edit: tried to clear up some majority/everyone generalizations. It's late and I need sleep.