I have owned an 01 xjr, 02 s-type (3.0), and 05 xjr. All three were very reliable and their quality were top notch.
To be honest, it is only my opinion but the S-type's rear styling got "commonized," and the suspension/transmission tuning got much less performance oriented after the middle of the model "improvements." I think McCallum tried to make it appeal more to the masses when he made the design changes.
Jags have always been known to have luxurious and supple rides, and yet still have that magical sporty feel when pushed. My 02 had just that. Later on whenever I brought my 05 xjr in for service and had later year s-types as loaners, everything felt really wrong.
Drive an earlier MY s-type (2000-2003) and you will know what I mean.
Nevertheless, Jags are still some of the prettiest and most elegant cars out there.