The 05- present LJ, TJ and the JKs all use the same transmissions. One is no really that much better or worse than the others. There is no HD transmission.
The TJ/LJ rubi lockers are decent but like anything, are driver destroyed. I have seen guys on 33s break them, and others on 37s have no problems.
LJs and TJs are not new, they are at least 4 years old now. There are alot of 08 JKs for sale now too. If you are buying new, wait till the 2011 model. Not one of them in stock form is worth 30k.
I have an 05 that I have had since the summer of 08. It gets used, but I would not call it beating on it. Its my daily, have to drive it to work on Monday sort of thing. But I don't see alot of my upgrades as expenses. If I only spend the money once, its well spent. I spent money on the poison spyder tub armour. Sure its pricey after paint, but after banging into the flares a little bit on some trees here and there, as it happens.... my tub is still straight. Most who do that with a TJ/LJ no longer have a straight tub. The tubs can bend easier than one realizes
I never had 4:1 t-case gearing. I had the NP231. replaced it with an Atlas 4spd. now I have 2.72 and 3.83 reductions. Much better for an all round vehicle. 2.7 for the mild stuff, 3.8 for crawling slow. 10.3 for just stupid slow. Was about the best mod I did.
If you go with an auto box, the NP231 is fine, and the Advance Adapters "Rubi-Crawler" box goes in nice and easy for another 2.7 reduction. No need to change drive shaft lengths or anything else.
I am running a Mopar 44 front housing, trussed lower control arm mounts, new HD upper pass side control arm mount, alloy shafts and ARB. Rear axle is a Solid Axle HD Dana 44 with ARB, alloys, and some Wilwood disk brakes. For what it would have cost to upgrade the stock axles to handle 35+" tires, this was actually a cheaper way to go and I think I ended up with superior axles than just upgraded stock.