Well I didn't want to quote the whole thing, it's in the transcript... but here's another morsel:
The anomaly isn't choice per-se, but rather created when some people, despite the choice they are given, reject the program. The more it happens (as in the more people wake up) the worse it gets (an escalating corruption of the code in the Matrix, presumably) until the emergence of "The One", at which point the contingency plan (as in the plot of the Matrix Reloaded) kicks into full gear and is supposed to end in the Architect's room.
Edit: Oh and btw, and coming back to Agents of Shield, you'll notice it's exactly what happens in the series with the framewrok. At first, when they capture Mai, Aida keeps trying different scenarios, perfect ones at the begining but Mai keeps rejecting them, until she comes to the same conclusion... The whole alt-history of the framework is indeed based on choice, in that Aida gives them the chance to change the one thing they regret the most.