When it comes to driveshafts, the LJ is a more forgiving than the TJ. I think you would be OK with the 3" lift, but its in a gray area that could go either way. Especially if you got 3 1/2+. I have adjustable arms and I believe I eventually adjusted my rear lower arms a little bit to tip the front of the pinion back down a little to keep the input shaft horizontal with the output shaft of the transmission. (This is the opposite of what you would do if you purchase a double cardon drive shaft.) I think I also adjusted the front a little bit to gain back a little bit of the camber I lost due to the lift. I think you could get away with stock control arms for a while, but you might get vibes at highway speeds.
One nice thing about a 3" spring is that it opens up more shock options. Typically with a 3" lift you will run a taller bumpstop so you can get a shock that is a little longer fully compressed. The issue I had with my 2" coils is that there are very few shocks that fit a 2" lift properly. The best options I found were the Bilstien 5100 for a 0-1" lift or the OME 2" lift shocks. Even the JKS shocks provided in the 2" kit are too long for the kit. The shocks will bottom out before you hit your bump stops. So you end up sacrificing up travel as well as destrying your shocks because they are bottoming out.
The disadvantage of a 3" lift is it can lead to needing driveshafts, and control arms. The control arms are also at a steeper angle which can have some negative effects on handling. Both the 2" and 3" should use a raised track bar bracket in the rear. A 2" lift can get away with the factory track bar up front. In fact even my 3" lift is using a OEM replacment tracbar.
In short, the 2" will maintain a little better geometry if you don't need the height. But it will restrict you a bit on shocks and tire options. But if you like OME shocks, I think they are a great option for a 2" lift. I've never run 32x11.5 so I'm not sure what height you will need or what offset wheel you will use. But either way a 3" will give more clearance and more options, but a 2" maintains slightly better geometry. I prefer the 3" lift and recommend a 3" unless you are certain you won't need to flex much and you will never run bigger than the 32". For a 33" tire, a 3" lift along with a body lift works best.
Another option, that is seldom considered is to get 17" wheels and run the 255/75R17 that the JK Rubicons used. This is a true 32x10 tire. It would actually be 1/2 taller than a 32x10.5x15 and only about a 1/2" shorter than a 33x12.5x15. But because its a narrower tire, you could likely run it on a 2" lift with little or no rubbing. The issue with this tire is that there are no hub centric 17" wheels that fit on a TJ. So you either need to run hub centric spacers with a factory JK takeoff wheel or get rims that are not hub centric. Its a much debated topic if hub centric is needed or not, as well as if spacers are safe or not.