There are many converters that allow you to use controllers from one console on another. You can rather easily find adapters to allow you to use a SNES controller on a Genesis, or a PlayStation 2 controller on an Xbox 360. However, I've never seen an adapter to allow use of a modern console's controller on a Jaguar. This seems like a particularly ripe area for development, given the high cost of the Pro Controllers on the secondary market.
One explanation might be that modern consoles don't have enough inputs to cover all the keypad buttons, but that's not really true. As we all know, the Jaguar Pro Controller repurposes keypad input for its new buttons, like so:
L(4) R(6) Z(7) Y(8) X(9) C B A
So if we were to use, say, a PlayStation2 controller (arguably the most popular controller for adapters) as the base, we could map the buttons like so:
L2(4) Select(Option) R2(6) L1(7) Start(Pause) R1(9) /\(8) (C) O(A) X(B)
That leaves keypad 1,2,3,5,0,*,# unmapped. But we have two analog sticks!
L3(*) R3(#) right analog left(1) right analog up(2) right analog right(3) right analog down(5)
That only leaves 0 unmapped, which we could throw on a left analog direction. But as far as I can tell, 0 is only ever used for music toggling. And my understanding is that there is at least one game out there - Battlesphere? - that supports analog joysticks (that are even more rare than the Pro Controller). So I think it would be more useful to kill two birds with one stone and map the PS2 left analog to the analog joystick input that Battlesphere supports.
What are the obstacles to such an adapter? The PlayStation2 controller is very well-documented, and given the insane prices on Pro Controllers, this seems like it would have significant demand.