Skyline to the Sea (and the other Bay Area or nearby attractions) are not in the same category as Grand Canyon, Sierras, etc. The Bay Area stuff is merely what you do in winter when the weather is not welcoming in those other places.
If I had three years I'd look at it seasonally:
1. Winter: Sure, stick close to home. Big Sur, Point Reyes, Skyline to Sea, Lost Coast all good options. Personally I prefer day-hiking over backpacking during this time, not only because the nights are long, but also because most of the really great Bay Area *hiking* spots do not have backcountry campsites (or do not have good ones).
For hiking, IMO the must-sees are: Climb Mt. Diablo from the north side/Regency Drive; hike the Steep Ravine Trail (Mt. Tam) to Stinson Beach; Big Basin waterfall loop (actually a good backpack trip; has some overlap with Skyline to the Sea but better IMO); Peters Grove; Pt. Reyes; the singletrack trail that hugs the coast between Muir Beach and Tennessee Valley. Moon's 101 Great Hikes of the SF Bay Area is the best reference book for these places.
If you are a trail runner then you will be in heaven here.
2. Spring and fall: This is the time to schedule some incredible trips to the desert. On top of Grand Canyon I'd say you *must* go to Southern Utah. Loads of backpacking choices in southern Utah but if I'd have to choose I'd say: Zion NP; Escalante River; Grand Gulch; or Canyonlands. Generally, March 15-May 15, and Sept 15-Nov 15, IMO are the best times to visit these areas, although be aware that elevations (and therefore temperatures) vary considerably from place to place.
Spring weekends, February through early May, are also the prettiest times to hike in the Bay Area. Everything turns green and the wildflowers come out.
3. Summer (July 1 - Sept 30): If I had a week each summer, for 3 years, in the West, I'd probably do this: One long trip in the High Sierra (anywhere south of Yosemite); one long trip in Washington State (North Cascades or Olympics); and one long trip in the intermountain West (Colorado, Wyoming, Montana, Idaho). To narrow this down, you can ask a more specific region-specific question on this forum. Here's a link to my recent query about Washington State:
As for summer *weekends*, I'd go to the Sierra. You can get surprisingly far into the Sierra wilderness even on a two-day weekend, if you are organized and get an early start. Tahoe (Desolation Wilderness, etc.) is my choice for a 2-day, only because it's a short drive; if I have 3+ days I will almost always go somewhere south of Yosemite and/or through Yosemite to the spectacular east side/highway 395 trailheads. Half Dome is a good 2-day weekend option; hike up it one day, see some of the other sites the other day. In the northern part of the state, the Canyon Creek trailhead for Trinity Alps wilderness is a 5.5-hour drive, good for a 3-day weekend; you just have to check that out, beautiful forest there.