1) not in the same class
2) not in the same size
3) cost of maintenance - altima is much lower (when i did diy on jetta, more than often i questioned their design being unnecessary unhuman; sometimes need special tools)
4) altima is more comfortable on the road
5) altima is quieter - jetta road noise is louder
6) both are unibody. jetta bottom is just a thin layer of metal sheet. i wish i could give it a higher score on safty but i can't.
7) jetta handling recalls has been just like toyota - knowing the problems existing but denies and denies until arms are being twisted. i am not sure what model/year you are buying, in the past, its diesel engines had big flaws and even to date it is yet to recall. (mine was covered by them eventually otherwise i would have lost 5k on the engine).