My best tip, is that if you have a table service meal, hit the restrooms there. They are usually less busy and cleaner.
Well, sometimes...see below.
My least favorite is the one just outside of Sci-Fi Dine In. It's not specific to the restaurant and seems to always be wet and disgusting.
The bathrooms at Sci-Fi are TERRIBLE, it is shared between sidewalk & restaurant traffic.
There is NO bathroom inside The Plaza, you have to leave the restaurant, walk down the sidewalk to a restroom, then re-enter the restaurant, if needed. A hassle with kids for sure.
The bathroom at 50's Prime Time is too small & cramped for the number of diners trying to use it.
For sure, Tiffins/Nomad bathrooms are very nice, but only a few stalls are offered.
I do like the public restrooms at GF, I think they offer better TP & hand towels than other locations.
IMO, WDW needs a different TP paper contract for supply. It is awful to pay this level of pricing & have a very poor TP product offered to guests. It also saves them NO money when each guests uses twice as much TP to get the same job done.