Two entirely different kinds of games, honestly. If you like first-person shooters, then you'll really enjoy JK. JK has GREAT level design and nice artwork, but then again, I think TPM does too ;)
TPM is for an ENTIRELY different kind of gamer, too. TPM is more for the casual gamer than the hardcore type. If you've played Unreal, Quake, No One Lives Forever and enjoyed them, then you'll probably hate TPM, because it's not a DEEP game at all. But, if you're looking for a fun re-living of the movie with lots of action and some puzzle-solving, TPM is a good choice as well.
You can find and download the TPM demo at:
http://download.cnet.com/downloads/0-10035-100-910858.html?tag=st.dl.10001-103-1.lst-7-1.910858)
Hey, just discovered that the TPM Demo has now been downloaded over 900,000 times! Not too shabby.