Ruling out the obvious.

Jets/Planes
The common aircraft in and around the Otay Reservoir area have very specific patterns.  Airliners coming into San Diego line up in an east-west approach over Mount San Miguel so that they can turn and land at the airport, which is positioned at a northwesterly angle.  They are like clockwork, and their navigational lights are very apparent and consistent.

There is also a skydiving area at the east end of the reservoir.  They use a couple different prop planes, but to my knowledge, they don’t operate at night.

Helicopters 
There’s one very specific trait about helicopters, and that is that they’re frickin’ loud.  They also have very recognizable navigational lights, although they might not always be the same colors or same arrangements.  And of course, if it’s the Ghetto Bird, then there will also be a spotlight.

Ultralight Aircraft
Ultralights have no navigational lights and are not permitted to operate at night.  Unless, of course, they’re smuggling dope in from Mexico.  But even then, I doubt they’d be considerate enough to install some lights.  They also sound like lawnmowers when they fly over.

Drones 
I know almost nothing about recreational/consumer “drones,” other than that they seem to be glorified remote-control helicopters.  Speed?  Lights?  Altitude?  Range?  No idea.  But we can put this on the list as a possible candidate.

EDIT: I almost forgot - motor powered parachutes have also been seen around here.  If anyone is dumb enough to fly one of these at night, then maybe they they really should get 'awesome UFO status.'  The problem is that they're incredibly slow.  And noisy.  Likely not an explanation for the things I've seen.  Unless it was falling out of the sky with a green light attached to it.