The sound quality of an in-line six is mostly a result of the cylinders firing at equal intervals, something that is not true of many V6s, for example.
The reason your Cherokee sounds funny is a result of the muffler used, and its location in the system, and the fact there's a catalytic converter in there somewhere also (presumably).
The muffler is the main culprit, and whether it's original or aftermarket, you can guess that its primary design constraint was that it be cheap, and that it reduce noise, not that it sound pleasing. There is simply not enough space in this forum to discuss all the ways in which an individual exhaust system can be improved, but suffice it to say that a good muffler engineer could spend months getting a good sound from a system like yours. What you would NOT want to do is to change pipe diameters to something excessively large - no more than 2.5" diameter - nor to simply change to an excessively loud muffler like one of the "Flowmasters." Ideally, you would not have pipes of equal length ahead of and behind the muffler, but you might benefit from adding a resonator in the tailpipe if you can squeeze it in to the rear-axzle "kick-up" area, like in some Ford Explorers.
My personal favorite in-line 6 exhaust sound comes from an E-Type Jaguar 3.8 or 4.2L, turning around 6,000 rpm in top gear...
Regards,
- R