The Catalyst only controls the Reapers while the Crucible is active.

I downloaded the leaked script again. Not just the ones found on the internet, I actually found the original leaked game files in which the lost lines of dialogue can be found using notepad to read through their XML strings. I stumbled across a nice detail Casey thought Mac should leave out back in 2012.
While the Catalyst scene was still too abrupt and unfitting for the climax in this version, these added lines actually remedy some of the things that people specifically complained about back then, one being that Catalyst takes away Shepard's agency whereas here he makes it abundantly clear that Shepard has to choose not becuase he must but because the Catalyst itself CAN'T. Then the final line, which I really like, it says that it won't control the Reapers anymore if the Crucible is turned off again. We know that if the player waits too long they get a game-over that says "The Crucible has been destroyed" so basically, Reapers are attacking the device. You could see that as if Shepard hesitates too much and Catalyst then decides to shut it down but I feel that might've been unintentional because I really don't believe Mac or Casey initially wanted the child to be evil. In fact, reading it again for the hundredth time it suddenly strikes me what they were doing.

This scene is the equivalent to meeting Vigil in ME1. I can't really prove this but I really feel like that was their motivation for doing it. The VI that comes when everything is dire and reveals the secrets of the galaxy, like a deus ex machina almost, except in both cases we were just about to win, but then this VI drags you to the side to tell you something important in the heat of the moment.

There's also a previous iteration of the same script found in another file called "BIOGame_Test_INT"
It's the same, the writing just isn't formulated as clearly as before. Also seen in this dumb line except it actually makes it abundantly clear what it's talking about, but it's hamfisted.

Although, I do like one thing about this sentence. It makes the connection between combining synthetics and organics into Reapers and Synthesis, a more harmless option that doesn't simultaneously violate the freedom and feelings of sapient beings, but the idea is still too late to introduce at the 11th hour, but for what it's worth it's at least clearer what the intention behind the concept is. As for the second line... hm, maybe I do understand why Casey wanted it more ambiguous, because the issue of how contrived and left-field this is to what is happening in the story, is just plain obvious. Lampshading it didn't help though

Control was also made abundantly clear as being something which Shepard overtook from the Catalyst.
Much better line than the "You'll control us but lose everything that you have."

Finally, there's also some rather dumb lines that I like here:

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Ultimately, though, these are just earlier drafts and therefore not canon. What was in the vanilla product was the canon then and then what is now in the Extended Cut is what is canon now, but it's certainly interesting to see some different formulations on the same ideas from prior to the game's release to get a sense of where these thoughts might've come from. I think I understand most of the changes but I still can't quite tell if the vanilla script was being so heavily cut down and made more ambiguous out of fear that people would find out how bad it was, from Casey's POV, or if they actually believed ambiguity would make it deeper or something. I think at this point we know the story behind all this, that they were very rushed, maybe egotistical or maybe out of resources and with all things considered Casey and Mac just tried to do the most efficient job they could at making an ending that wasn't just the simple "We beat our enemies, hooray!" to get it prepped for cinematics and complete the product, but all this rushwork made them unable to stop this navel-gazing in time to realize it really wasn't panning out well at all.