If I'm traveling by myself in a roomette, the in-room toilet in the V-1 sleepers is a non-issue, because I sleep in the upper bunk. This allows me to avoid sleeping by the toilet, and also be able to use the seats all night.
Traveling 2 in a roomette is another matter. Using the in-room toilet requires exiling your roommate into the hall while you're using it. Obviously a problem at night. When I did traveled with somebody, I just put on my shoes and walked down to the coaches to relieve myself. It's a bit of a nuisance, as you have to walk through at least 3 cars before you get to the first coach, given that Long-distance Amfleet cafe cars don't have a restroom. I guess when I ride on a train with V-2 sleepers, I'll be able to use the common restroom in that sleeper even if I'm booked into a V-1.
However, when all is said and done, the in-room toilet isn't really all that gross. The whole roomette gets cleaned before you use it, and you're the only one using it. The actual commode is very well covered by a lid that serves as the first step to get up to the upper bunk. If you didn't know it was there, you would never guess that it covered a toilet. The main thing to consider is that if you use it while the train is standing at a station (especially one with high-level platforms), be sure to pull the window curtains fully shut!