Well, this is a bit of a touchy topic, or it can be. There is some controversy not only about the length of time Yamaguchi studied with Miyagi, but also whether he studied with him at all depending on whom you ask. Certainly the Goju-kai side says he studied about 5 years with Miyagi. That said, Yamaguchi did study with Yagi, one of Miyagi's top students, so I'm not sure if it ultimately makes too much of a difference. (Not sure how long the Yagi connection lasted...)
I am not a big fan of Urban-descended Goju-ryu. While I think he deserves a lot of credit for popularizing karate on the East Coast in his day, I see little in USA Goju today that resembles what I practice myself.
As for what characterizes JKF Goju-ryu from Okinawan Goju-ryu:
- Yamaguchi added a series of H pattern forms called the Taikyoku kata. I believe they were likely lifted from Shotokan karate and then were modified to add Goju stances and techniques such as shiko dachi. I think they have 12 total which seems like a lot of basic forms to me. Some older tae kwon do systems practice variations of the Shotokan Taikyoku kata; they're generally called 'kibon' or 'kicho' hyung.
- Practice of kobudo is generally more prevalent among Okinawan Goju-ryu
- Generally, hojo undo (traditional body strengthening exercises using tools like sand-filled jars or stone rods - http://en.wikipedia.org/wiki/Hojo_und%C5%8D) is found in Okinawan Goju-ryu but not JKF Goju
- Various small variations in kata such as use of angles in the end of the Gekisai kata
- JKF Goju-ryu uses one steps; Okinawan Goju-ryu tends to use two man kata bunkai sets which explain the meaning of the kata
- JKF Goju-ryu tends to be more sport-flavored; they participate organizationally in the various tournaments, including WKF