I believe that throughout all 3 games Shep was exposed to enough Reapers to have some degree of indoctrination. I don't see a need to pinpoint a certain time that her indoctrination level was suddenly detectable, by the VI for instance. While I didn't exactly suspect hallucinations at the end, I was very skeptical of suddenly seeing everything in a new light. And I did think that TIM and Saren each must have had their "Aha" moments when they joined the Reapers. And they were wrong.
But I believe the game was intentionally written so that you can interpret several ways. You could also make an argument that Shep really was special, for real this time. Nobody had ever built the Crucible before, so it could be the key to controlling them. Or, if it really "changed" them, the key to merging all life forms.
I don't think there will be another ending because I think they purposefully wanted to be ambiguous. But to me, the right answer will always be dead Reapers. I didn't come all that way to suddenly share the vision of those psychos from the first two games. I don't know if there will ever be an official "true" ending, but I believe in indoctrination. However I try to forget everything after my flashback of Joker, Anderson, and Kaidan because the rest made no sense for any ending.
And I don't remember any talk with Kaidan about some tropical planet. Was that only if you romanced Liara or something?