I have both. My 2000 Wrangler has the dual top option, and my 2009 wrangler has the hardtop with removable roof panels. I’ve owned both Jeeps since they were new.
The softtop is stored on the vehicle (although you have to remove it to put on the hardtop). Raising or lowering it is not especially simple. I think the first time I ever tried to do so on my TJ, it took me 45 minutes. Everything has to go on in a particular sequence. But now with practice I can take it up or down in fewer than five minutes. And yes, it’s noisier when I’m driving.
The hardtop with removable panels is kind of cool, but not nearly as much fun as an open top Jeep. It also takes more time to remove or replace the panels than it should, in my opinion. Truth is, I don’t bother removing them very often. Newer Jeep tops may be easier to operate.
Other observations. The hardtop is essentially permanent while the softtop will need periodic replacement. I’ve heard it will last about five years but that assumes it’s mounted on the Jeep all the time. If like me you keep it stored while running the hardtop for long stretches at a time it can last much longer. My softtop is going on 19 years old and its still in fine shape. The windows are a little scuffed although I’ve heard they can be polished. I haven’t bothered.
If you run your Jeep with the top down I strongly advise getting a sunshade. There are some that don’t require attaching any mounting hardware. They just use bungee cords. And you can keep them in place permanently with either softtop or hardtop raised or lowered. I use Spiderwebshade.
In summary, I like the flexibility of having both, especially since I have storage space for the hardtop. If I had to choose just one I’d go with the softtop because it’s so much easier to remove and I love Jeep cruisin’ with the top down.