Rancho Penasquitos canyon is approx 11.5 miles roundtrip on an out and back trail. You could make it longer by running some of the mountain bike trails north towards SR56.
Rancho Santa Fe golf course trails for Sat or Sun long runs. Woodchip trails with loops around the course after running the equestrian trails through the neighborhoods.
San Pasqual is good.
8 mile Loops around Mission Bay are good, but only some portions are soft surfaces.
I always enjoyed running the beach on low tide from Del Mar Powerhouse Park south past Blacks beach into La Jolla. You can pick up the trail to head up to Torrey Pines also.
Lake Miramar in Scripps Ranch is a 5 mile paved loop marked every quarter mile. Good for tempo runs.
Mission Gorge is ok, but a little farther from Escondido.