Depends on how you intend to use your jeep. If you are like most of us you will do 98% of your driving on the road so I suggest a quality lift , like AEV or Teraflex, that have very good road handling characteristics. If you live in an area that has some more challenging off road opportunities I would look at Rock Krawler. As for lift height, again, depends on lift manufacturer and JK vs JKU.
If you are running a JKU you can go with a 3.5 AEV lift and, most likely, not have to change anything else (MAY have to modify exhaust or change front drive shaft for clearance...I did not on my '14). AEV uses brackets to keep the geometry within tolerance.
Of course, as others have said, most any 2.5 lift will be the best bang for the buck and you won't have to worry about geometry etc.
I am very happy with my AEV and I installed it myself. After install I took it for alignment and it was still within specs. In fact, it drove straight as an arrow until after the alignment...now it pulls slightly to the left...have to take it back in. I suspect they were adjusting for the camber of the road and put too much in.
Hope this helps. Continue to do your homework and talk to people. Google different combinations and select images...there are lots of photos our there to help.
This is mine...AEV 3.5 RS w/ 35" Nitto Trail M/T on 18" Fuel Wheels