If I replace it with a soft top, how well do the soft tops work during the winter? ... if the soft top is the better option, then which one?
I've had mine for almost 3 months now (stock "premium" soft top), and I can tell you that that it is livable in the winter. It's quiet, holds heat well, and doesn't baffle or flap at all. However, there are cons that you need to consider:
a) it's a PITA to clean with all the salt and road grime that works it's way into the cloth;
b) the rear window sucks to unzip when your hands are freezing;
c) you can't just squeegee the rear window at the gas station or use Windex and a rag - it has to be washed clean to avoid massive, deep scratches... ask me how I know
d) the rear window plastic will snap if you try to fold it up over the roof when it's too cold... again, ask me how I know! Luckily for me, Jeep covered it under warranty no questions asked;
e) you have to be diligent about not letting snow pile up on the top as it will be quite hard to take off if/when it freezes and because it may damage/rip the cloth (I think it would take a lot of snow to do that, though);
f) you have to use soft-top conditioner every now and again to prevent/reverse UV damage and aging;
g) if you get a soft-top that began life as a soft-top and then you want to get a 2nd hand hard top, you'll have to install the hard-top wiring (defroster and wiper arm) and washer hose, which can be tough if you don't have the patience for electrical work.
Basically, getting a soft-top over a hard-top is like getting a cat instead of a dog... it might be more convenient when you want to leave for he weekend, but there are a lot more maintenance in he long run! If you can get a hard top from the start, do it. You'll pay less for an aftermarket soft-top, you'll have the wiring/hose there when you want to put the hard-top back on and you won't have to worry about complaints like mine!