Bad King wrote...
Except the vision was made by protheans (probably a small number of survivors who had witnessed the collectors) and was most likely them trying to show the transformation over a short length of time (I doubt it was real footage). Compare it for example to a real life animation of evolution in action- there are animations on youtube of single celled organisms evolving all the way to humans (a proses which took billions of years) but which is compressed into a 5 minute video.
For a start, you're now contradicting yourself by saying this "footage" proves it being a short length of time by comparing it to an animation of something which takes 3.5 billion years.
Anyway, its not like the Reapers just fly into the galaxy and take a look at the protheans and think "you know what would make these guys better? 4 eyes and no digestive system. Lets also get rid of the superfluous DNA and 3 chromosomes for the lulz" and with a wave of a tentacle thing, it was so.
If the Reapers could really do stuff like that, then Sovereign would've had no trouble taking the Citadel (You know what would make you better at your job, Shepard? NO LUNGS! *waggle tentacle*)
No, what actually happened was the Reapers come in. Reap. Realise the protheans are incompatible (this is centuries later) and think about what to do with the surviving members. (most of the protheans now being unusable goo) So the Reapers take their indoctrinated slaves and turn them into Collectors. The only surviving members of Protheans now are sleeping on Ilos and have no knowledge of this process.
Shepard's extra vision you get is just the revalation that collectors used to be protheans. A bit of extra information added to an existing memory (lets not forget that the exact same image(s) appear in the ME1 vision without the change into collectors), not actual footage of what happened.