My current bikes have 28mm tires without fenders or 23mm with. The 28s ride much better and give me more stability with rough pavement and especially pavement cracks. I am also very concerned I will pince flat the 23s even though it hasn't happened. I don't really notice much difference in speed but both are kevlar belted so neither are "fast". Thats why I'm looking at getting a bike with better clearance so I can fit my 28s with fenders for wet weather and 35 studded for snow.
For commuting a lower BB will make it easier to put a foot down and give a little better handling but you will have to be more careful about pedaling in turns. A custom builder should be able to make a sport tourer with long reach caliper brakes. This should give enough clearance for 28 or 30mm tires with fenders. If I didn't have to deal with snow I would probably be looking at something like an Ant Light Roadster ( http://www.antbikemike.com/lr.html ), it sounds like you want something more like the Club Racer ( http://www.antbikemike.com/clubracing.html ).
Craig