The time span you've described covers 2 different models of Wrangler. Until 97, it was called the YJ. Then from 98 until 2006 it was called the TJ. I don't of any big problems with either of the models. I will say a few points though:
1.) Whatever you do, DO NOT buy a 4 cyl. The gas mileage might seem like a good idea, but there is literally no power being made from that engine. I'm pretty sure I could produce more power with on onboard pedaling system.
2.) The YJ is a leaf sprung suspension, while the TJ is a coil sprung suspension. There are easy and cheap ways of lifting both, it all just comes down to which you feel more comfortable with playing (as far as suspension goes. IE: installing the lift yourself). I will say that I'm a HUGE fan of a coil sprung suspension because if offers more articulation without having to have a massive lift. Also, I personally feel that the coil sprung TJ has a better ride quality than the leaf sprung YJ.
3.) Earlier YJ's have a 4.2L inline 6, but I would try to get something a little newer that had the fuel injected 4.0L. They are VERY reliable engines, and have tons of torque. Also, I'm getting 17 mpg hw and 15 in town with my 4.0L with 32" MT's. And I'm definitely not easy on it.
4.) I would try to test drive both a YJ and a TJ. The interiors are the same except for the dash layout, and personally, the YJ's dash layout sucks. It's very small and low, yes, but there are more ways to expand and add accessories to the TJ dash without it looking jerry-rigged.
5.) As far as transmissions go, the AX15/NV3550 manual or the 42RLE are all great trannys. I like having a manual in the Jeep because that's what it should have, and they are VERY easy to drive. The autos are reportedly "stronger" than the manuals, but I'd rather spend a couple hundred replacing a clutch than a couple thousand replacing a whole tranny.
6.) As far as upgrades goes, anything over a 3" lift will require a SYE (Slip yoke eliminator) because the stock shaft will start to vibrate when pulled out too far from a larger lift. The SYE kit itself is $1000. I have a 2" lift (with cut fender flares and no front swaybar) with 32" BFG KM2's and have gone everywhere my friend with a BII (SFA swap) with 8" of lift and 35's has gone. All it takes is proper driving style.
7.) If you look for a TJ (which I would strongly advice doing), I would really try to find one with a D44 rear axle. They ALL came stock with D35 rear axles, but it was an option for sport models to have a D44 with LSD (limited slip) (which luckily mine has). If you plan on getting anything bigger than 35's and you have a D35 rear, you'll either need to upgrade axles shafts, or do the smart thing and put in either a D44 or a Ford 8.8.
That's all I can think of right now off the top of my head, but if I think of anything else I'll reply.