If i had a hardtop i would run it during the winter only. It would def keep the heat in better than the softop. That said, I dont have much of an issue (if any) heating the jeep in the winter. On the coldest days it may take a bit longer to heat and may not get as hot but its never been so ineffecient as to require me to wear a jacket and gloves while driving...on the coldest days i may have to keep a sweatshirt on while driving but it hasn't been worse than that AND that's with half doors and on really cold days. Benefit with the hardtop would be the insulation.
Summer time, nothing better than being able to just pull down the top at will and put it back up whenever you like. If all you have is the hardtop, you would have to ride with a bikini top for those surprise showers, or have to go through the hassle of wrestling the top on everytime the weather looks like it's gonna be crappy.
Jeffy mentioned putting the top on at night, yes it is a pain, but once you've done it a few times it really isnt that bad and you sort of memorize how to do it. I can do mine in the dark no problem now, BUT if it cools down enough at night it becomes a pain cause the fabric constricts. My advise would be to go ahead and run the softtop during the summer and put it away during the winter.