Perhaps, with Protheans messing up Reapers' plans and then Sovereign and Collectors getting destroyed, Catalyst even then started realizing that organics are more than it thought and decided to see what else they can offer, for which it needed to give them some space to breath? I find it very plausible, considering that it said about "new variables" during talk with Shepard, which, apparently, should have appeared at the moment something in a usual cycle routine went wrong, in this case - Protheans reprogramming the Keepers.
Also, they probably saw something special in Shepard. Like Leviathan who said that "His confidence is singular". Apparently Shepard alone changed both Leviathans' and Reapers' views on organics, so he/she might have been spared so they could see how he/she fares.