Have you figured out the one way car rental fee?
Are you spending any time in Denver or just renting a vehicle there?
The best plan that I could come up with would be to fly to Denver and then take the Amtrak CA Zephyr (morning departure) from DEN to Grand Junction. This would take you through the most scenic spot I know of on any of the Amtrak routes: Glenwood Canyon. Rent a vehicle in Grand Junction. The best dinosaur sites in the US are in the eastern half of Utah IMO.
You can visit the dinosaur quarry near Vernal or a prehistoric museum in Price. Arches NP near Moab is also worth the trip. Return your rental to Grand Junction and then either fly or take the train to San Francisco (Emeryville).

You have to understand tom - he thinks no trip is worth taking unless 1) part is by train, and 2) there are no rental drop off fees (He must have been very traumatized in a past life by an expensive rental car.

IMO A very reasonable 2 week trip would be Denver to Mesa verde to Bryce/Zion to Lake Tahoe to San Francisco. About 1500/1600 miles depending on short sidetrip(s)

Oh - and yes, you probably will have to pay a drop off fee (which will cost less than multiple train train tickets)

Points of interest between Mesa Verde and San Francisco include Monument Valley, Arches NP, Bryce NP, Zion NP, the Grand Canyon, Canyon de Chelly, Sedona, Las Vegas, Death Valley, Sequoia NP, Yosemite NP, the Gold Rush area on Highway 49, and Highway 1 on the Pacific Coast.

HTTY

I'd add Canyonlands NP while you're near Arches to HTTY's list, otherwise that hits the spots I'd like to see.

You could head to the Great Sand Dunes on the way to Mesa Verde. Make reservations to stay at Far View Lodge in the park at Mesa Verde.
I don't have the route in mind but if Tioga Pass is open, you could go through Yosemite on the way to SF.

>> . . . Sequoia NP, Yosemite NP, the Gold Rush area on Highway 49, and Highway 1 on the Pacific Coast.<<

I totally agree - The main reasons I omitted those are 1) w/ only 2 weeks - and IF they spend much time in the SW parks they will be semi-rushed, but mainly 2) in May they might have to go around via Bakersfield to get to Yosemite. And I don't wish that drive on anyone

If Tioga Pass is open then I'd definitely/100%/absolutely recommend Yosemite (but not Sequoia since that involves than same butt ugly drive)

Yosemite > Hwy 49 > Lake Tahoe and on to SF - Or - Yosemite > the coast > SF

You are all awesome. Love the train idea, but will save that for a romantic trip sans children The car is for mobility, independence, and ability to travel at anytime we choose (even overnight). The drop off fee is a bummer, but will have to take the hit...

Will look at all these options... sounds like Utah is virtually unanimous in votes, as opposed to clipping the southeast corner on way from CO to AZ...

One request: please try not to call the city San Fran. Thanks.