Hum, I've got a "new" theory to think about (actually it's a mix)
After the coup when you have Anderson and Hackett on the com they say something like the Crucible generates enough energy to defeat the Reapers and they are sure the Catalyst controls how to release it so it doesn't wipe out anything else.
Now we assume the Catalyst is something on the Citadel but if it's in fact a determined person? This especially makes sense when we look at the low ems segment. We have only either destroy or control, and Shepard is desperate. More desperate than needed and therefor it has very destructive side effects.
Higher ems means Shepard is less desperate, but used more time, more time to be influenced.
Now the actual Catalyst in this case would be Shepard, the choices would be just a manifestation in her mind for the player to choose. The guardian however can be two things: the part of the psyche that is broken (there are numerous references to that, especially if you start a game without importing), and maybe controlled. Another option would be a manifestation of Harbinger in her mind (more "classic" IT) who tries one final time.
Another plus to this theory is indoctrination preys on turning the victims wishes into the wishes of the Reapers. The Reapers want synthesis, or at least "survive", so a Shepard who is desperate and determined to destroy the Reapers would never choose Synthesis. It can only come up when Shepard is more relaxed, less on guard, and can be implanted with suggestions. I couldn't think of any other explanation where it would make sense to get Synthesis with more EMS. It has to be a complete mind game for it to make sense, for which the only explanation is: Shepard is the catalyst.
And it's not just evidence for this in the last bit, we can see that whereever Shepard goes people believe in her. Even when not agreeing (VS on Horizon who even goes so far calling Shep a god) Shepard gives hope and gives people who nearly given up strength. Look at the people you pick up for the squad. Everyone starts out like they've given up, but it's Shepards determination which gives them strength, the same determination she uses to activate the Crucible.