BB height is always an interesting discussion. scott is so correct about some of this being preferential. I absolutely hate serious pedal smack, and some bikes have it in spades...others don't. There are so many factors. On the handling issue with some tall bikes and many riders, there is often a problem with a decently tall BB. I had an '03 Bullit with a very tall BB...forget the number at this point...but I had installed a longer shock and fork. Though it didn't quite carve like my Nomad, I had no problem with fast cornering. I've ridden some other tall BB bikes and didn't have much cornering issue with them either.
I got to thinking that perhaps it was because I was used to riding very tall long travel dirt motors. While not a 100% comparison, you have to be very conscious of where the CG of the dirt motor is when you lean it into a corner aggressively. The height of the bike is less of an issue when you have the CG planted directly over the tires and into the bike's footprint...if you get my drift. I basically do the same thing with my mountainbikes, right or wrong. I think lots of people are more into steering and remaining as upright as possible. Of course you have to lean to some degree regardless of skill or fear factor, but leaning into the corner right at the point of the bike's CG and tire contact point being in line diminishes the impact of the BB height. It's a little bit of balancing act, and it can bite you once in awhile, but you can get used to it.
Funny thing...that Bullit didn't pedal all that efficiently, but you could pedal that sucker through some pretty nasty rock gardens without pedal smack. On the last trip to Moab with a riding buddy, his frame broke on his Spec Enduro the second day out on a 10-day trip. I bring the Bullit as a backup bike, and even with a 170mm single crown fork and the OEM sized 8.5 X 2.5 shock, the Bullit is known for a tall BB. My buddy rode that bike the rest of the trip, noticed the serious lack of pedal smack in many of the technical, rocky trails there, and absolutely loved it. As already stated...people are different.