My spouse and I are also taking our first trip on the California Zephyr in a few months, and went through the same dilemma. We decided on two roomettes, for the reasons everyone has listed above - especially the fact that the bathroom in the bedroom is REALLY small. I much prefer using the regular shower and toilet rather than the mini-phone booth in the bedroom, aside from the "wet bath" issues.
Also, as lonestar648 said, watching out the aisle window in a bedroom is not easy. You're basically looking straight sideways, and the view isn't nearly as good as when you're right up against the window. With two roomettes, we're not really concerned about going to the Sightseer Lounge to watch the scenery - we'll just switch sides to the other roomette. Amtrak made it really easy to make reservations too - I expected to have to jump through a lot of hoops, talk to a supervisor, etc. to get roomettes across from each other, but the agent handled it without issue. I've had a much more difficult time getting airline agents to give us adjoining seats.
As to the luggage - there's a large and fairly secure luggage space downstairs in each car. While it's theoretically possible to steal luggage from that area, I've never heard of that happening and I think most people on this forum would leave their luggage there without hesitation. This is especially true if you have upstairs roomettes, where you'd have to drag your luggage up a very narrow staircase with some tight corners. And when you got your luggage to the roomettes (or bedrooms, for that matter), there really isn't any space big enough for full-sized suitcases, & they'd just be in your way all the time. You could just set them on the seats (if you have two roomettes, that's four good seats for only two people), but that would make it difficult to sit in the same roomette if you want to see the scenery out one side of the train.
On the positive side, each roomette has two steps that lead to the upper bunk. Each step is about the right size for a small / medium size piece of carry-on luggage. If you have two roomettes then you won't need those stairs (since no one will be sleeping in the upper bunk) and those steps make a good place to store a carry-on bag. You can also slide a carry-on under your seat (which is fine during the day but impossible to get to at night). If I were you I'd plan on leaving any big suitcases in the luggage area and bring smaller bags into your roomettes.
(Probably not, but it's fun to think about)
