Posted this comment in another thread. Included it below as it seemed relevant here too.
I've long had a fascination with the Jaguar, but only recently played one and got into collecting for it. Part of that fascination stems from when I saw a picture of the controller back in '94 or so and thought 'what the hell is that!?'.
Having played both the black and grey ones, yes there are definite differences, as you say Kill_Bill. In fact I was really struck by how much of a difference there was.
The Jaguar has it's faults, and the controller is often cited as a prime example, but, like many others, I was pleasantly surprised when I first held it. It was pretty comfortable. For it's time too, the '3D' moulding was a definite step up from the mostly flat SNES, Mega Drive, 3DO controllers too. I also think the flak for C B A ordering of the buttons is unfair: Nintendo had been doing it B then A for years and, to my knowledge, hadn't been criticised as much as Atari were for doing the same thing with the Jaguar controller. I also don't get the criticism regarding it being huge and chunky. It's actually quite light and is not dissimilar to other controllers both before and since other than they tend to have a gap between the two 'prongs' you put your fingers round, while the Jaguar uses that for the number pad.
Even though I was pleasantly surprised with the how the controller felt to hold, I have to say that the D-pad and the buttons were sources of disappointment. The D-pad was too small, too shallow, wasn't 'clicky' enough to really give feedback on how you'd moved it and the same criticism could be made for the C B A buttons. However, having played both the black and grey button versions I was taken aback with how different they feel with regard to these points. I can't remember off the top of my head which one was better (the black button one I think) but it made such a difference to the feel of playing the system as it basically resolved those issues for me.