I have done both upstairs and downstairs, here's the pros and cons:
Upstairs Pros
Bigger window
Private shower
Sink in room
Dont need to use the stairs
I find the upstairs rooms "brighter" than the rooms downstairs.
Upstairs cons:
The toilet in your room is really just for #1. You definitely will want to take anything else down the hall. Also, the bathroom is just a wet room, so if you take a shower, consider the toilet soaked and out of commission for a while.
With the lower bunk folded down, you cant access the sink or the door without climbing over the bed.
If you have the top bunk, you're about 14' off the rail, every undulation of the track is amplified up there.
Downstairs pros (family bedroom)
More room (full car width)
Because the door to the room is perpendicular to the bed axis, you can still move around with the beds down.
The downstairs corridor is roomier to move around.
Less traffic in the corridor
There's 3 bathrooms down there + the shower (which is bigger than the one in the rooms upstairs)
Track motion is less noticeable.
Downstairs Cons:
Track noise is more noticeable
You get 2 windows, but they're not as big as the picture windows upstairs. Also, if you leave your compartment door open upstairs, you've also got a window across the corridor, so you technically have 2 windows
No bathroom in the room, but its not a major negative (see above)
The closet is basically useless
If the attendant is in a roomette upstairs, getting them to come down can be a challenge, especially when its busy.
The view is basically track level, the viewpoint upstairs is definitely better. This is not so bad if your plan is to camp in the sightseer all day.