If I may, I would like to provide input with out answering your question "What is the best year"
I have a 2005 rubicon, Please do not get me wrong, I have wheeled this thing pretty hard.
The differential lockers have both failed internally because of the little hose clamps on the rubber hoses that go from the barb that goes through the diff case and the air operated pusher. The hose has slipped off, I have replaced the little clamp and it has happened again and again. I have looked for a better clamp, changed that and replaced the hoses, big pain in the ass and you can not get the factory oem clamps.
Next, the axle shafts them selves are junk, I snapped each one and replaced with superior axle parts,
The u-joints are junk, I ended up with Alloy u-joints.
Each time you blow a u joint the axle will tear the shit out of the three 12 point bolts that hold the unit bearings on. Order these in advance and carry a spare set with you. When the axle comes in contact with the bolt heads the rotation backs the bolts out, so if you are trying to limp to the trailer, you suddenly will not be able to turn once the bolts get backed out.
I call the front locker the 300 dollar switch, every time you engage it you break a 300 dollar part,
The front axle tubes are know to be easily bent, I have done this, their is very little room to truss on the driver side as well so it is a known hazard.
The upper control arm mount that is welded to the axle tube is made out of tin foil, and will snap off. You will need to spend 250 dollars to get a new curry unit and weld it to the tube.
All in all in my opinion, the dana 44 axles that come stock in a rubicon are junk.
I have owned several dodge trucks from 72 through 94, I believe 13 different trucks, I have beat a few of them stupid drunk. I have never had any thing other than a bad u-joint or a broken stub axle.
Avoid stock rubicon axles they are for show, and no go.