It does let you reject the whole premise, though.
It doesn't give you specific dialogue to attempt to call BS to the Catalyst and have a discussion about it sure, but that's hardly a complaint specific to the ending of Mass Effect.
Even the games with the best of dialogue I've had cases where I didn't have an option for something that seemed like a perfectly logical reaction to me. That's just the limitation of video games at work there.
I've played games where I ended up not having an opinion either, or just wanting to walk away (Dragon Age 2 comes to mind)
But what I'm talking about is more than that. It's the situation in toto
Why was Shepard, formerly bleeding out and unconscious, suddenly able to walk and talk?
Why does the Catalyst resemble the creepy child Shepard had been dreaming of?
How did Shepard just happen to pass out on the Magic Space Elevator?
How does shooting a pipe turn all synthetic life off?
WTF is "organic energy"?
Why can't Shepard just throw The Illusive Man's body into the magic green beam to achieve Synthesis?
What assurances does Shepard have that the Catalyst is not lying or trying to indoctrinate Shepard?
Why can't Shepard contact Hackett or Joker while chatting with the Catalyst
These are just questions about the situation Shep is in, beside the point of whatever nonsense the Catalyst is blathering on about inevitable robot uprisings, "final evolution of life" (someone's played too much Pokemon between cycles), and how organic life isn't worthy of existing alongside synthetics.