2 door unlimited (LJ) gives more room in the back. Drawbacks of the longer wheelbase may come into play while offroading. Aftermarket parts can be a little harder to come by (seems some with LJs have trouble finding tops, etc).
If I had it all to do over again tho....I'd do a 2006 Rubicon Unlimited(LJ) in a second.
Differences between a TJ and JK...heres the can of worms. TJ's interior and exterior are a little more simple. Some like it. Some don't. Me...I like it, but can't argue that the JK's inside is nice and has more creature comforts. I believe JK's offer a little more stock clearance as well, but don't quote me on that. I'm not so sure that a TJ's ride is worse than a JK's...I've never noticed a difference in ride comfort.
Rubicon doesn't effect you getting a 6 speed. Thats just 2005+. Rubicon is giving you lockers, suspensions, wheels, rocker guards, etc. Keep in mind if you want to add lockers yourself later, your looking at $2 - $3k.