I guess I'm in the minority. I love the sky option in my Autana, it was the main reason I got it, and if I ever get another RTT, it'll have it too. I think it's the best feature on the tent. But I'm also in SoCal so rain isn't really a problem here, your area might be different.
I use it almost every time I use the tent. In the morning, I'll unzip the panels and let all the light in, and if there's any condensation it dries out instantly. Without the sky panels, the interior of the RTT is pretty dark and dreary during the day, and it can get stuffy in hot weather, even with all the windows and doors open. It's especially noticeable if the tent has the covered entrance.
If I need better weatherproofing there's a rainfly that covers the entire top. I don't really see a downside to it other than price.