It nearly is always just the few small changes that make all the difference in the way a bike looks. That's what makes it a bit frustrating that the bike did not look like the V&H one from the factory to start off with.
Single seat, narrow tail section. Why couldn't this be stock? Harley sells lots of bikes with no passenger accomodations and as this is their sportiest, why not?
The lower handlebars would be great too.
Granted, some of these changes are really easy to do in your own garage - the pipes and handlebar. But the 17" wheel is pricey. The tail section would need work done to accept tail lights etc. Do-able, butt again annoying as it should have looked like this anyway!
I think HD is the exception to the rule of making a bike that fits "Everyone". They offer single seat models but this is something no other mfg really does, particularly on a volume-based machine. Yes, companies like Ducati turn out single seat versions but these are for limited-production (IE: limited customer), rather expensive models.
So I think it's unreasonable to expect HD to make the XR1200 a single seater. I do not see single seat FZ1's, ZX1000's, etc.

One of the biggest complaints you hear today about new bikes is their horrible exhaust systems. As riders, we've been tossing exhaust systems since the day of the flood, so I fail to see how their choice in an exhaust system is a big deal.
The lower handlebars probably make the bike more uncomfortable. 'Nuff said about that. A 600lb pseudo race replica? Yeah, right.
The ONLY reason the V&H bike has a 17" front rim is to accept race rubber. That's it. The bike handles WORSE with a 17" wheel. Seriously, there's an article in Cycle World right now that supports this statement. The bike handles fine, why does it have to have a 17" rim??

As I stated earlier, the V&H tail section simply does not look "Better" than the OE tail section. It looks Japanese, that's all.
Throw the V&H system on a stock bike (Something many owners will do anyway) and you have a winner.