I like the rooms in the Cal west tower best. The bathrooms are fully enclosed, inside they contain the tub/shower, toilet and vanity. At MSS the bathrooms is split into 2 parts, one "room" contains the tub/shower and toilet and the other area contains the vanity. The standard room at the Cal also has a table with 2 chairs so isn't much different than MSS.
If I had an option I would rather stay at the Cal. Parking lot is connected to the hotel so you don't have to go outside or get wet walking from the parking structure to the hotel. The walk to your room isn't as far as at MSS, especially if you are coming from the FSE. At MSS you have to walk all the way to the back of the hotel, take the elevator and then walk the corridor back to your room. For me I find it easy at the Cal to get to my room. The noise from the trains or freeway isn't as loud at the Cal as at MSS (IMHO). Unlike other posters, if you have a MSS room near the tracks it may bother you if you are a light sleeper.
But I don't think you will go wrong with either hotel, at MSS just ask for a room facing south so you don't encounter the noise from the freeway. In the Cal west tower, ask for a room facing west so you get some view. I wouldn't recommend an inside room at the Cal, you are facing either the east or west tower so no view other than the rooms in the other wing.
For me my first choice for downtown is the Cal and the second choice is MSS so both places aren't much different.