Pines to Palms is a great road, and, depending on where you're going in San Diego, 2.5 hours is a reasonable estimate. We do this drive every few weeks (Dad lives in La Quinta), and really enjoy the scenery.
The climb out of Palm Desert is a bit challenging, but it's only about 10 minutes of the drive - the rest has good visibility and isn't too twisty.
It will be much cooler when you get up to Anza - if you plan on getting out of the car you may want a light jacket - the temperature is frequently half that of the desert!
It's also a good idea to stop for fuel in Temecula - for whatever reason gas is $.30-$.50/gallon less there than in either San Diego or the desert.
Taking the 78/79 generally takes much longer, even though it is fewer miles.