This is not a question of which vehicle is more capable or better, but rather which one is preferred because of interior and ride.
I currently have a 94 YJ that is in excellent mechanical condition and has never been abused. I have all of the tops for it and it is set up for towing and winching the way I want. HOWEVER, the frame is rusted through, the body is rusted through in the typical places and the body mounts are either shot, or the rubber totally GONE.
So, my choices are 1) patch and get by; 2) do a frame off; 3) or buy another one.
Obviously 1) is cheaper but certainly not as secure a vehicle. Would cost about $1,000 to patch and fix some things that have to be (new radiator).
Option 2) is to do a frame off. I have located a vehicle with pristine frame and tub that is rust free, but has some significant physical damage, especially at both rear corners. I can get most of the odds and ends I need and the cost would be about $2,000 by the time I get it on the road with a 2.5" suspension lift, new radiator, etc.
Option 3) is where the question comes in. I can sell what I have for about $1,200 as-is. If I take the $2,000 of build cost, I am at $3,200 that I could spend on a replacement vehicle. Certainly, that isn't going to buy a TJ, but I can get into a 1999-2001 TJ for in the vacinity of $5,000. And I am going to have well over $1,800 of time and skinned knuckles before the frame-off is done.
From a YJ standpoint, I think I prefer the simplicity and access of the YJ interior (dash particularly). However, the high air ducts seem good. The coil suspension seems like it would be smoother and easier to lift modestly.
So, my question to those who have had and used both a YJ and TJ, what is your finding regarding the interior amenities and ride? Is the TJ significantly better and worth the extra. From a capability standpoint, I would consider them to be equals, if equipped equally, so that is not a factor.