The center column on my Bogen 3001 did compromise stability, even when fully down because it added in several joints that did not quite lock tightly. The overall flex in the system was worse, even if the center column was all the way down. This is probably not true with nicer tripods such as a Gitzo.
I'm currently using a Feisol CT-3301N with no center column and a Kirk BH-3 ballhead. I really enjoy the combo and have had great results with it. I considered the RRS BH-40 and Markins M10 as possible alternative ballheads, but ruled them out because of price.
I've since noticed that Kirk is selling new BH-3's on Ebay with slight factory blemishes for $235. That's a great value, if you ask me.
I haven't been bothered by the rotating legs, you just have to learn which order to open them in. I've found that I'm just as fast with my Feisol as I was with my Bogen. Actually - to be a complete nerd I just timed myself setting up and collapsing my Feisol. It takes me 12 seconds to go from folded to full height, or to collapse all three legs back again and fold the tripod up.