TQCoach,
I feel if you can afford a 2nd gen model, a Rubicon is a great choice IF you can find one that is not priced much higher than other models, but I know not everyone agrees totally with that plus you can't always find a Rubi for the same price, they are out there but you have to be patient and sometimes willing to drive or fly further to get one.
So how about some more practical general advice to help your question might be if we can make a list of things that most everyone could agree on. 100% of us will never agree 100% on hardly anything. However, there are things that most of us know to be true that would be helpful to share with you.
A few that I can think of off the top of my head include;
1. Check for rust.
2. Check for rust. Seriously... Frame, body, fenders, windshield frame, you name it! If at all possible take it somewhere that it can be put on a lift and really look it over good.
3. Watch out for idiotic mods done by clueless previous owners. One already upgraded with a lift and what all can look cool and can save some money if it's mods you would do anyway but check them out or have someone who knows Jeeps check them out (or if all else fails get lots of pics and post here) to make sure that the PO who did the mods wasn't "clueless" and did more harm than good. You don't wanna be fixing other peoples screw-ups.
4. A second generation 03-06 model is more refined inside and nicer as a daily driver (have friends with early models who wish they'd gotten a 2nd gen model) but they will also cost more on average. There is nothing wrong with the 1st generation (97-02) but the second gen is just more refined, especially the interior, instrumentation and controls, nicer seats, etc.
5. Many models, esp. 1st generation generation models seemed to come with 3.07 gearing. Avoid it if you can. Several of my own friends are dealing with this now. 3.07 gears SUCK pretty much all the way around and especially if your son may ever want to go with larger tires, which he will, can almost promise it. If you look you can find 3.73 gears in those same models for the same price. So know what gear ratio your getting. If someone claims they have upgraded the gear ratios refer back to #3 and ask who did the work. If they said "them and their buddy" did it themselves in their friends garage... uh, yea... There are certainly guys who can do it properly in their own garage, but a lot of people can't and literally did it by watching a YouTube video on how. That's one I just heard recently when I went with a friend to look at a '99 model that was for sale and it was clear the guy was an idiot based on the work he did that we COULD see, didn't even want to imagine him and his drunk buddy in their garage setting up gears properly using YouTube as a guide some Saturday night.
6. They often cost just a little more but the 4.0L inline 6 is the way to go. Yes people get by with the 4 cylinder models and many are happy with them but the 4.0L is where it's at, can't say it any simpler than that. The 4.0L can handle about anything he can throw at it, wont feel like he's using "two mice on a treadmill, a rubber-band, and a piece of cheese on a string dangled in front of them" as a power-plant if he want's to put on larger tires. Plus will hold it's resale value much better should he ever decide to upgrade later.
7. There was some models (someone please chime in and specify, my mind is blank but I want to say 00-01 models) that had a serious issue with some faulty heads cracking. So may want to steer clear of those models. I know Jerry Bradford knows and maybe he will chime in and make sure I'm right on those years.
8. As someone eluded to earlier the 05-06 models had an OPDA issue, also sometimes known as the "screaming monkey" syndrome so you should not consider one of those UNLESS you spend a LOT of time doing research on the subject and watching a few YouTube videos BEFORE you go to buy one of those models. So you know what you may or may not be getting into. If the problem hasn't reared it's ugly head the fix is actually simple and easy and only about $115 the last I heard, but you need to know what to look and especially listen for on the 09-06 models if you look at those.
9. If your looking at 2nd generation models with Automatics, including Rubicons, the 2003 model had a shallower transmission pan which lead to a larger chance of over-heating.
10. OK, Someone else take a turn here, I know I'm forgetting some...
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