So I'm pretty familiar (as a pax, not a pilot) with weather and its impacts at SFO, where low ceilings or the wrong winds play havoc with the schedule. You can't shoot parallel approaches in sub-VFR conditions, and you have crossing traffic in the middle of the field, all that good stuff. It's way less obvious to me and/or I'm less clueful as to why this impacts a single-runway operation like San Diego (KSAN).

KSAN has a single east-west runway, and I don't think I've ever deparated or arrived on 09, it's always runway 27. But when the fog/marine layer lingers into the morning at SAN, things get delayed and backed up. This seems a LITTLE odd to me, because I would have expected that all of these arrivals and departures are instrument anyway, and they're all going the same direction, and there aren't any other (at least major) airports in the immediate vicinity... so why is there reduced throughput when the clouds stick around through the late morning?

I have to assume that somewhere there's a weather threshold where you have to increase the separation for takeoffs and/or landings? If so what is that threshold and why (again if it's all instrument operations anyway?)

I'm quite sure there are good reasons, I just can't figure them out intuitively and don't know the regs well enough to know where to look. ;)