Oh yeah... I hated my CJ's top in the cold. My TJ was slightly better. The sailcloth came out a year after I bought my TJ. The JK top isn't too bad. The cold still affects it. I had to put up my rear window this morning because of the rain. I was cussing it out while pulling down on the bows to ease up on the zipper.
You're right about the side windows. I'm not a fan of that either, but, by the looks of it, it was a design necessity. It also looks like you lose the sunrider option. I must admit to liking that about my top.