TransitGeek
Service Attendant
I gave this advice to a poster in the main forum, and somebody suggested I post it up here as well.
As far as tourist-friendly cities, those three will about run the gamut in the state. However, California has plentiful natural wonders to offer. At the very least, if you've never been, you should spend some time in Yosemite National Park. (Amtrak provides service there, but it is an *early* departure from LA- read 4am. From SF the last connection is 7am. You might plan it between Los Angeles and San Francisco- that is, if you're willing to leave LA at either 1 or 4 am.)
Disneyland is a pretty easy connection either from Los Angeles or Anaheim. From LA, take the Metro 460 express direct. From Anaheim station, take the Anaheim Resort Transit route 15. (More info at metro.net and rideart.org respectively.)
The bus between LA and Bakersfield is a 3-ish hour trip. I'm not sure how long the ride is between Merced and Yosemite. The ride to San Francisco is a quick 20 minutes right over the Bay Bridge.
As far as time in each city, it depends on what you want to do. If you hit any museums, zoos or amusement parks you'll probably want to allow time for each of those. Disneyland is easily seen in a day, and I wouldn't bother with California Adventure unless you're getting in free. (Often, specials will allow you to do just that.) It's basically three big rides and a lot of gift shops. Do catch the San Diego Zoo, it is pretty incredible. If you can arrange transport, also catch the affiliated San Diego Wild Animal Park in Escondido. They have huge, multi-acre enclosures which replicate the animals' natural habitat, and you can see them wandering about as if they were still in Africa or Asia. You can get there on transit- from the Oceanside station (Amtrak/Metrolink/COASTER/SPRINTER), take the SPRINTER to Escondido transit centre and then NCTD #386- but I don't know how the schedules will work out from you. It's pretty far out there.
In LA, the Getty Museum is pretty impressive, but perhaps not kid-friendly. The Griffith Observatory is also very cool, and they have an amazing, recently rebuilt planetarium- but unless you like hiking, the shuttle only runs on weekends. On the plus side, you get some fantastic views of the city- including the famed HOLLYWOOD sign (which is smaller than you think it is)- from up there. California Science Centre and the LA Museum of Natural History are both very nice, and located in Exposition Park. By the time you get here, we should have the Expo light rail line up and running, which will put these attractions within an easy train ride from Union Station. They're already pretty transit-accessible, though. Hollywood is a tourist trap, but a tourist trap with easy subway access. Grauman's Chinese Theatre is a block west of Hollywood/Highland station, while Hollywood/Vine station provides access to the walk of fame.
I absolutely love San Francisco, and if it weren't for a certain pesky graduate program I'd move there in a heartbeat. Everything there is 100% transit accessible- don't worry about it for a second. Check out Alcatraz and walk across the Golden Gate. Go to the California Academy of Sciences ($3 off if you show your transit pass.) When you ride the cable cars, stand on the sideboard- it's one of the few places in North America you can still do that. Get a burrito or taco in the Mission (but maybe do it for lunch? Some find the area a bit scary after dark. Our favourite place is called El Farolito, on Mission just north of 24th, less than a block from the 24th St. BART. Don't book a hotel in anything described as the "Civic Centre" area- this region is affectionately known as the Tenderloin and is essentially the city's skid row. Hotels are cheap, sure, but not worth it.
You may also consider heading to Sacramento. California's capitol city is a rather pleasant place, hemmed in by rivers on three sides, with pleasant parks, the quirky Midtown neighbourhood, Sutter's Fort (the place that began the gold rush), and the State Railroad Museum (part of tourist-trappy Old Town). Sacramento is an easy Amtrak trip from pretty much anywhere- two trains daily on the San Joaquins line plus innumerable Capitol Corridor trains from the Bay Area serve the station, as well as the Coast Starlight if you end up riding that. All of the tourist-friendly places are pretty well-served by Sacramento Regional Transit, including their two light rail lines, but note that frequency and service span drop off *quickly*- just a mile or so into the 'burbs and the buses run hourly, stopping at 7pm.
Hope this helps, and I hope you enjoy the trip to our fair state. We could use the tax revenue.