Let me know what you find. I'm interested to know if there are any significant differences or if they're nearly exactly the same.
I'm not JOT, but as I have a 2000 version and a 2009 version, I can tell you what the differences are (at least one the two I have):
-The 2009 version still carries the 1999 copyright date on the foot/hoof, and the overall color of the beast itself has a definite yellow tint to it.
-The toenails on the 2009 version are painted solid gray, as opposed to the 1999 version, which has some worn gray on the nails. The kneecaps on the 1999 version are also painted in a worn gray, with the 2009 version's kneecaps being unpainted (remaining in the same overall shade of yellow as the rest of the beast).
-Both have the "liver spots" along the side, although the 2009 version is a bit more pronounced and the pattern is slightly different.
-The 2009 version uses a more muted set of browns on the saddle and saddlebags when compared wih the 1999 version (the 1999 version looks more like a toy, if that makes any sense).
-The 2009 version looks a bit "dirtier" than the 1999 version, especially noticeable on the back of the head and neck.
-The eyes of the 2009 version are white with tiny black dots, whereas the 1999 version has pink eyes with tiny black dots.
-Qui-Gon, obviously, is the 2009 Evolutions version with what, to my untrained eye, appears to be either a new and/or repainted head or a modified neck to avoid the giraffe look of the Evolutions release. The 2009 Qui-Gon has some difficulty sitting correctly on the saddle due to his front skirt piece, but it can be made to work with some effort; the 1999 version is an action feature-laden sculpt that sits on the saddle perfectly (which makes sense, as the two were designed to be compatible from the start).
-The stance on the legs seems to be a bit wider on the 1999 version as well, although that might be due to age more than anything else. Both stand well and need no additional support, although you will likely need to fiddle with the legs the first time you stand it up for the proper alignment.
Overall, I have to say that I still prefer the 1999 version, although the 2009 version is nice, too. I'm still displaying the 1999 version on my TPM shelves, but I picked up another SL Obi-Wan to display with the 2009 version on my ROTS shelves, and it looks great. 6.99 for an extremely difficult to locate beast along with what is debatably the best Qui-Gon Jinn figure we've gotten is a hell of a deal, and I highly recommend picking it up, even if you already have the 1999 version.
On a side note, the Saga Legends/2008 30AC Mustafar Obi-Wan with the ball-jointed hips works well on the Eopie, although he has the same difficulty I mentioned with Qui-Gon regarding the front skirt piece. I'm still fiddling with it so he'll sit properly, but it will work with a little effort.