Steering wheel controls can be retained, you just need to buy a wiring harness that provides that capability. PAC and Metra both make one. I believe that the phone button will not work any longer, but you can reprogram it to do something else.
Factory bluetooth can not be retained, but a lot of modern head units come with Bluetooth capability along with their own mike. Effectiveness varies; the one on my JVC head unit is so bad as to be virtually unusable.
Security is obviously a concern with a soft top vehicle like a Jeep, one of the main reasons I went for the JVC is because it has a removable faceplate. That's slightly unusual for a double DIN head unit, Pioneer also do one. Alternatively, you can get locking security covers which fasten over the head unit, but there's an argument that they're simply an advertisement that you have a head unit worth protecting. When I replace my head unit, which knowing my predilection for buying audio toys is likely to be soon, I think I'm probably going to get one of these:
which is just a dummy faceplate that makes your radio look like a very low end piece of factory crap.
As to brands, you pay your money and you take your choice. There's no one brand that's better or worse suited to installation in a Jeep. What features do you want, and what's your budget?