I've got a 4 door Rubi with 35's, 4.10's, and a 6 speed.
The 3.8 V6 is what it is. It makes enough (just barely) horsepower, but it makes it higher in the RPM band than I would like. Drive one, see if it's enough power for you. If it's not, then look at other vehicles because the "more power" options on the JK are pretty limited. You can bolt on a blower, or you can do a hemi swap - there's not much else out there to improve the engine.
I haven't had any problems with axles at this point...but I don't wheel as hard as some other folks. Yes, the ball joints are less than great...but then again, ball joints are a replaceable part that WILL wear out on any vehicle. To my mind, they fall in the same category as brake pads, unit bearings, and u-joints. As far as the front axle housings go - if you're worried, then beef them up. You can get inner sleeves, outer sleeves, gussets for the c's, and trusses off the aftermarket. Cheaper than buying a Currie axle
From the people that I know who have a good knowledge base, you're probably fine running 35's on the Rubi D44 if you don't really beat on it. If you do want to get rammy with, then sleeve it, truss it, gusset the C's, add heavier ball joints, and put in a set of Chromoly shafts. Or you could buy a D60 and upgrade to 37's