i have a black supatrem and a Ferrari yellow one, and I love them. Never tried the jr, but I doubt Fulltone would put out something very inferior.
I've seen pictures of people's boards with the smaller model on them, and never seen any complaints about them. Not sure if they've had the big box version to compare, but apparently it's a keeper for them.
It would be interesting to hear what the differences are, but I'm keeping my big boxes.
I have an original SupaTrem and last years Supa Trem Jr. I dont experiment with the wave shapes. I just dialed in the slowish trem I always used in my original. They sound extremely close to me, if not identical to my ears. I definitely prefer the new box design of the Jr.