This is a nice option for running just inland from Mission Bay, east of I-5 and north of I-8. Combine the pleasant trails of the University of San Diego (not to be confused with UCSD in La Jolla) with the 6+ miles of trails in adjacent Tecolote Canyon Nature Park. Some of the trails are easy dirt roads/gravel paths, but there are some hillier and more rugged options as well.
Longer Run/Options: Dip down to Mission Bay and the paths along Tecolote Shores, Fiesta Island, and Southern Shores Park. This would be a run with lots of variety: waterfront, university campus, dry canyon trails! Note: Tecolote Rd./Sea World Dr. are not so pleasant for running.