Biggest advantage I can see would be having less physical components, hence less crowded mobos, hence good for smaller-than-ATX boards like mATX or ITX. Would be less parts and drivers to go wrong or have incompatibilities as well.
But is that really an issue today, when everyone uses NEC or VIA chips, seriously? I see your point, but I still don't think it will affect the end user anyway.
It seems like Asus
are both capable to make mini-ITX boards with dual chip chipsets and loads of features, and the abcense of a separate USB3 chip wouldn't make enough room for regular RAM slots anyway.
If less parts are that important I'd suggest using eSATA only, as AFAIK it doesn't need any additional controller chip even in an external HDD.
My impression was that Intel have included a USB3 chip in their reference designs for SB motherboards, ie Intel suggests the manufacturers to add it, but that doesn't really change anything from how it's done today.
Sure, it would be great to have USB3 integrated, but in the end it would be one of the least important features of a board. It doesn't make new boards "much more exciting", that's for sure.