Suzuki has left the 109r untouched other then paint since its release. This has been virtually the case with all of their bikes since the mid 2000s. They had a lot of opportunities to up the ante with the 109 but they chose to do nothing. The same can be said about the r3 but the latest models are very stout and can make serious power reliabily. You simply can't make a m109r compete with a r3 when it comes to a drag race, dollar for dollar invested the r3 will win. You can't make a m109r outhandle a r3 because it lacks the lean angle to make fast turns. I would have ripped off the exhaust and dumped a 109r taking turns I have with my r3, and I am not a pro rider. Riding 2 up the r3 has that by a long shot, and there are a lot of shock options to make the bike handle anything you want.
All other muscle bikes suffer from the same problems the 109r does, they are good at 2 or 3 things and suck at the other. The Vrod was somewhat of a joke at one point, but it has far surpassed the 109r and with aftermarket parts has become quite a threat on the street. However it is not a good bike for big guys, or riding 2 up on long distances. Its lean angle is also limited although seemed better then the 109. The ducati diavel is a unruly beast that I like, but Its civility on distance trips is non existant, and it is ubsurdly expensive. I rather get a busa or a zx14 and set it up with a nice seat for a lot less (I fit better on them too). The vmax is a beast as well but it sacrafices too much for power and performance at a cost of comfort.
The R3 is the bike I wish harley would have built (I live in milwaukee and its harley country here). A very solid cruiser that has a unexpected power plant. 200hp to 240hp is a easy possibility, which is unreal out of a cruiser engine with reliability. If you want better handling shocks/forks/carbond wheels/sticky tires will give you a lot. If you want better touring bags/windshield/seats will give you that. Harley gets everything right but the power. 35K for a bike that puts 90hp to the tire is hardly thrilling. Once again the Vrod is bad ass but is a small bike and not that great at trips.
I think all of the top 5 muscle bikes look good. 109r, diavel, vrod, vmax, R3, are all bad ass bikes. However only one of them is good at everything I want in a bike, thats the R3.