The Chicago to San Francisco route (the Zephyr) is probably the more scenic of the two, as it crosses both the Rockies and the Sierra Nevada. I can't speak for the rest of the journey, but the ride between rode the Reno and Oakland in the winter is spectacular.
I've never ridden the Chi-LA train, so I can't comment too much on the scenery. However, the ride could be very scenic heading through the north of New Mexico and Arizona.
The Sunset Limited (LA Florida) does parallel the Gulf Coast for a short section of the trip, but otherwise, it looks to be a very long, very flat, and rather dull ride. Again, this is just based on word of mouth, but I would probably recommend against this one.
The services on all three trains should be essentially identical. The coach seating is actually very comfortable (large pitch, legrests, lots of recline). There is a lounge car, in which movies are shown from time-to-time, or commentary is offered from route guides. There is a full-service dining car, although my experiences with food have been quite varied.
If you're going to be travelling with a companion (or just appreciate a little peace and quiet) I would recommend investing in a private compartment. They are pricier, but for a two-day journey, I don't think it's a bad investment. The deluxe rooms offer a little more space and a pint-sized private bath/shower. The economy compartment is really nothing more than two seats which face each other and can be made into bunk beds for the nighttime.