Haven't ridden a Custom but my wifes Honda Shadow has a front wheel similar to the custom (though not as big in diameter)
I prefer the larger wheel myself, it's more stable, smoother, doesn't follow grooves in the road. To me, it's a better choice for the type of distance riding and commuting I do, just an all around more comfortable ride.
However, my wifes bike has a lot more road feel, and that skinny tire effortlessly lays into corners; I've heard that about the 900 custom vs the classic as well. I sometimes steal my wifes bike just because of how nimble and fun it is! Of course; it likes to follow grooves; which my wife hates!