Pebble Beach beats PacDunes in a few areas, namely:
1. the quality of its three shotters
2. its famous long two shotters (8-10) are, as you say, world class, while PacDunes' 7th is in need of companionship
3. As targets, Pebble's tiny, pitched greens are harder to find and/or recovery to. Some like the 12th and 17th at Pebble are tiny out of mistake but in general, Pebble's greens represent a more exacting challenge for the approach shot, not withstanding the great 6th green complex at PacDunes.
4. Pebble's cliff line is better as it is less linear and thus the architects could better incorporate it into the playing of the holes. The cliff is "only" an issue on the 4th, 11th, and 13th holes at PacDunes whereas the cliff confronts the golfer in different ways at Pebble, highlighted of course by the 8th approach and 18th tee ball.
Conversely, PacDunes offers greater width off the tee, greater angles of play, its larger greens afford a greater range of hole locations (and accommodate a greater range of type approach shots) and its varied green complexes such as those found on the 2nd, 6th, 7th, 8th, the great 10th glued to the ground, etc. throw a lot of different looks at the golfer.
Still, Pebble's raw challenge + beautiful setting is a tough combination to beat though PacDunes competes with it like few others. Overall, PacDunes is most deserving of GOLF's #26 world ranking but I'll be surprised if it ever gets as high as Pebble's.
Cheers,