I'm with Bayo on the idea to keep things simple - or in this case, making a group of things have common features.
I. e. making all "alien missions" similar either in shape or in color, just like all Phalanx installations etc., in order to keep the globe tidy.
Since radar towers already have unique shapes, and the same is to expected for SAMs, I think groups with equal or similar colors but dfferent shapes are the way to go.
That would mean that all Phalanx installations would be white/blue, for example, but with different models. Crashed and landed UFOs could be round orange pins, with bases being square orange pins. And then, if you zoom in, there are the symbols to distinguish e.g. between crashed and landed.
Other colors should then only be given to special things, like a big red pin for a story-based alien attack.
EDIT:
Something like this for the aliens. Important missions would be the same pins in red and/or flashing.
Or using the exclamation mark, if we want to be blunt about it.