My vote would go to Yosemite. May is peak waterfall season, as all the snow melting flows into the waterfalls. It is truly awe-inspiring! Bring clothes and non slip shoes for wet weather. The spray off the waterfalls in abundant.
You can pick up a guided hike at the visitors center, or go on your own.

Been to G.C 7 times now and wont get tired of it, ever.
Sure you can fit Zion and Bryce to make a mini Grand Circle which will make your time even more worthwhile.

I'm a lover of US National Parks as we have very little to compare here in the UK, so I tend to come out west every year.

I stayed in Yosemite for 3 days a few years back and since i'm a hiker, did the most iconic hikes. However most of the views are visible from the valley below and unless you go to hike, not a lot else happens. The trees limit visibility somewhat and the granite all around becomes uniform. Don't get me wrong, I loved it, but it is not somewhere I'd return after seeing once.

G.C just blows your mind away given its size and various viewpoints. I've had spectacular sunrises and sunset pics, floating clouds bringing heavy snow flurries which then pass leaving fantastic rainbows. Hiked the trails to give below rim viewpoints which I believe is necessary. Even N and S rims are different.

Trust me, you wont regret it.

With only three days and leaving from San Diego, I wouldn't recommend trying to see the Grand Canyon, Zion and Bryce. You'll be spending too much of your short time traveling to and from parks. (But if you could add a few days it would work.)

Here is a link to hikes in Yosemite: http://www.yosemitehikes.com/

You'll have to do some research and decide which park is more appealing to you. I'm in the Grand Canyon is ok but I've gone to Yosemite eight times in the last two years camp. I think that the granite is gorgeous and the views from the high country are quite different from those in the valley. Even when you're looking at, say, Yosemite Falls, views from both the Valley and from Taft Point are quite different.

But only you can decide which one would be best for you.

PaulRabi,
You stated in Feb. when answering a question "What park should I visit. Yosemite or Grand Canyon." Your answer was these were the 2 of your favorite top 3. Curiosity has me wondering what is your 3rd in your top 3.

"Go to San Fran and see yosemite"-- Yes!

I don't think the spray from the falls will be abundant this year.... we've had very little snow and Tioga Pass is already open. My parents are there today and I will report back.

While I love both, I would choose Grand Canyon first. Unless you want to see Las Vegas, I would not fly there. Phoenix is more convenient. Check out Sedona, stay overnight on the way to the South Rim.

My fav 3 parks are Yosemite, Zion, and GC. I like the former two because of the accessibility - it's easy to get to all points in the park without extreme effort. My definition of extreme is pretty extreme - I'm willing to hike 15-20mi per day...

I did a 2 week rafting trip through the GC last May and consider it a trip of a lifetime experience. If you look hard through binos you can see little dots up on the western viewpoints as you run the rapids. :)

I have one or more return trips to the GC envisioned, but it takes a lot of planning to make a trip like I want. Gear, permits, vacation, travel companions, etc. The 1st trip I'm scoping out is a 4 to 6 day camping trip where you hike in from the North Rim to the river ~50mi below Phantom Ranch. Hike in is one day, a few days at the river at one or more camps, then a hike out.

Very good idea to fly to Phoenix, to drive to the Grand Canyon. You'd go through Flagstaff on the way?

I'm with Dayenu,

Fly to Phoenix and visit Grand Canyon NP, not the helicopter to the west rim. Stop for the night in Sedona unless you get into Phoenix before noon, in which case drive up to GC. Check on lodging ASAP. If they say they are full in GC, make a reservation that you can cancel in one of the Tusayan motels or at Cameron Trading Post, then call back for in park lodging and keep calling as people make reservations a year in advance and it is so nice to be able to watch sunrise/sunset without having to dodge deer and elk on the road after dark.

If you decide on Yosemite, you are late for lodging there too, so get that settled now and maybe that will be the deciding factor.

Wess --
Since you asked, the answer is Yellowstone.

If you pick Yosemite, try to make a reservation - hotels may be sold out, and to stay outside the park with such a limited time is not good, too much driving.