Nice looking Jeep, Danny.
Especially like the photo with the passenger side off the ground.
I'll try to answer what I can of your questions...more folks will probably chime in tomorrow.
1) All the JK's here come with the 3.21 gear ratio. What is the max recommended tire/rim size before I have to re-gear? I don't want to re-gear a new car as I might lose warranty.
The 3.21 gearing is a slug. Chrysler shouldn't even offer it on the Wrangler, but they do. However, the 3.6L Pentastar engine – with its extra hp and flatter power curve – eases some of the pain. You should be fine with 33" tires, as long as you watch the backspacing on the rims (4.5 is ideal.)
2) Is it recommended to go for wide tires/rims on a stock suspension? If yes what size? The biggest problem we face in the desert are popouts
Again, that's going to be governed somewhat by the backspacing on the rims. You can go with wheels that are wider than stock, but you'll want to make sure what you buy isn't going to rub in hard turns, etc. When you narrow down what rim/tire combos you like, throw 'em out to the masses here on WF. Somebody will be able to tell you about them.
2) Has anyone tested the new JK on a steep climb?? The only problem I have had with my TJ (also auto) was that everytime I was climbing a high dune, I lost power and had to turn down. I am hoping the 12 JK doesn't have this issue - please share some real life experiences
The '12 has more power than earlier model years, but with a 3.21 gear ratio and larger tires it's not gonna be a dune buggy. That said, the 2012 should still outperform your '05, power-wise.
3) This will be my daily driver as well..so what brand of tire do you guys recommend? I loved the Cooper HTs and I have heard the Geolanders are good as well.
The Coopers are good, from what I've read. I live in the Upper Midwest, and need a tire that I can use on the road year-round (we get a good bit of snow in winter), so I went with Goodyear DuraTracs. They've got a fairly long tread life, and work well in almost all conditions.
For desert driving, I can't say...maybe somebody from the southwest and west will chime in with some suggestions.
Anyway, hope this at least gave you a start.
Welcome to WF!