Also another common argument I see is that Shepard can only be shown to have long-term indoctrination symptoms, and that IT suggests it all suddenly 'speeds up'.
Well, look at many long term illnesses. They can progress very slowly, over years, barely noticed. Then suddenly they flare up, have rapid symptoms and then kill you. Since indoctrination is a biological effect on the brain, it makes some sort of sense that long term effects would slowly change the way the brain thinks, and then when it reaches a certain stage it will then have sudden and dramatic effects as control is taken from the victim.
Not to mention certain conditions can accellerate conditions. Like, I don't know, having the oldest and largest Reaper who's been taking personal interest in Shepard for the last two years show up in person, landing only a few hundred meters away?