I'll second Yosemite & SF over LA. Grand Canyon and Death Valley are also great. Vegas, not so much, but YMMV.
When I was looking at Amtrak prices (NY to Washington DC), it was cheaper to hire a car and drive than take the train (2 adults with 2 suitcases). Figure about US$100 per night for accommodation, including taxes. You can do it for less, but you'll probably not sleep too well... bed bugs and rowdy neighbours and too close to the freeway.