I have a 2002 TJ. I don't know where the 'unreliable' stuff comes in. It's BS, plain an simple. If you are really worried about it, get a new one - they all come with 7 yr/70,000 miles on the powertrain, and there isn't much in a Wrangler that ISN'T powertrain
I've had 5 jeeps in my familty, a '02 TJ, an '94 ZJ, a '97 ZJ, a '97 XJ, and a '01 KJ. The only one that had ANY issues was the KJ (Liberty), and that was mostly first-model-year related(recalls, etc). The '02 ZJ was my dad's company car, the other ZJ (Old Grand Cherokee) was killed in an accident, the XJ (Cherokee) was ALMOST killed, never the same, and replaced by the KJ. The TJ runs like a top.
Jeeps DO hold there value (at least Wranglers (YJ and TJ), XJ's, and CJ's) very well. Grands don't hold their value as well. Don't know about Libertys. You'll never get 'upside down' in a Wrangler - you will always be able to sell it for more than you owe on it.
If you need a little more room, you can look at a Wrangler 'Unlimited', which is a stretched TJ.
I'd stay away from the 3 speed auto. It's 1985 tech., pure and simple. The 5 speed is bulletproof- that's what I have. Also, you are correct in wanting the 4.0. The 2.5 is fine at 'rock crawling' speed, but lacks on the expressway.
Your model options are basically X, Sport, and Rubicon. The more you pay, the more you get off road. Any of them will run circles around any other stock vehicle you can buy. I'm pre-rubicon, so I have a sport set up as well as you can. If you aren't going to be doing any 'Hard' off roading, an X will probably suit you just fine. Keep in mind that the Dana 44 axles (std front and rear in a rubicon, opt. rear (get it) on sport, N/A on X) are not compatible with ABS, so you can't get it.
Don't worry about what tires you get 'standard'. X's get smaller tires than Sports or Rubicons, but when I bought mine, they'd swap them for you, even if it wasn't an 'option' on the model you were looking at. You're dealer will probably do the same.
Hopefully you aren't stuck on the $5-6k range you listed later. You can't touch a Wrangler in good condition for that. Either get a mid-70'+ CJ, or use it as a down payment. Remember, because of the resale value, you'll never be 'upside down'.