As I believe out of all proposed protocols Satoshi's is still the most powerful, I would suggest that any change to the semantics on nSequence be gated by a high bit or something, so the original meaning remains available if/when resource scheduling and update flood damping are implemented. That way people can try it out and if miners are breaking things too frequently by ignoring the chronological ordering people can abandon protocols that rely on it, and if they aren't they can proceed and benefit from the greater flexibility.