Jag is inferior to N64 in every way possible, by the way.
Fixed that for you.
There is little redeeming value in the Jag. Any good game on it is found better elsewhere. The N64 has a solid collection of decent titles, though; it does 3D better than the Jaguar, it has a better controller than the Jaguar (and that's saying a lot considering the N64 controller), and the game library outstrips the Jaguar by a large margin. There is no comparion.
But we know how much you fetishize the console design, that toilet design, so go you. 
The Jaguar may not be superior in every way, but there are still many good things about it that it has over the Nintendo 64. I can't list them all, but a few off the top of my head include:
Better controller for 2D games.
Controllers don't wear out quickly.
More buttons and support for overlays.
Better library of 2D games.
"Real" or "traditional chip sound. Not just that sample shifting stuff which only gets worse with age.
Like every other 32-bit gen console, it has a CD-ROM.
Superior video quality, including RGB output. -the poor video quality of the N64 combined with mandatory filtering really makes it hard to make things out. Which is why I recently ordered one upgraded for RGB output.
System linking ability, allowing for multiplayer games of up to 128 players.