Ah, a thread I can fully contribute to.
I've attended both high schools (San Marcos for my first two years, and Mission Hills for my last two and also graduated from there in '06).
San Marcos is nice, especially for being an old school....but Mission Hills is where you want your kids to go. It opened up during the 2004-2005 school year so everything is still pretty new and state of the art. And unlike San Marcos High, Mission Hills provides programs such as Fire Technology, Criminal Justice, Culinary Arts, and Health Academy. The campus is much more up to date and a LOT cleaner.
As far as the gang problem at San Marcos High, I personally never noticed it when I went.
Which school will your kids be attending for now? San Marcos Middle or Woodland Park?