what are these circumstances outside of apex-faction cards? I'm pretty sure there aren't any, as the insert for D&D had to include a "what are the rules for installed-face-down runner cards" section.
Back on topic: I agree with other posters, most of the mechanics listed either a) are purely deckbuilding related and thus add no complexity to actual gameplay, or b) are pretty simple to understand, such as flip IDs and facedown cards.
I feel they have a long way to go before complexity creep becomes a problem (though to be fair this is largely because the base game itself is quite complex, so it would take a lot of creep to really ruin what's good about the game) and I have a feeling that rotation will deal with that pretty well.
All that said, I wouldn't be opposed to a "netrunner 2" a few years down the road. buy-in cost for potential new serious players is getting pretty daunting, and rotation will only slow this problem, not reverse it. Plus it would give them a chance to revisit some of the biggest design missteps that happened in core and elsewhere.