I hope this is a conversation about the older body styles and not that new Wrangler/Cherokee junk they produce now?
If talking older, Cherokee if you are going to drive it for more than just weekend fun, Wrangler if just a trail toy.
Not much suck like driving a Wrangler daily. They handle awful, brakes are terrible, unstable on the highways,more so if you have a lift, no power, if you have a soft top only, cold in the winter and not so cool in the summer sans removing the top and doors.
Cherokee's are pretty comfortable for how capable off road they are. Plus, the added storage and rear seat comfort (if yours is a 4 door) is pretty descent. Still handle like crap, are slow and brakes are meh. Miles above a Wrangler for comfort though.
Resale favors the Wrangler of course given the same year/miles, but again, it is about your intended use.
As far as. Takes and bigger tires for lifted vehicles....get a set of EBC yellow stuff brake pads for the front for much better stopping power than anything the auto parts store chains carry.
Very soft pads but you get a lot of dust although you
Wanna stop.