I dont believe the 06 hrc was so different from rossi's bike that it can be called (quite a different beast). If you have knoledge to prove otherwise than please post and i will concede.I cant see that their was anything that radically different apart from pneumatic valves?
The 06 Honda didn't have pneumatic valves, Honda were testing them in 2008, if you recall when Nicky ran out of gas at Assen and lost 3rd place to Colin on the line.
Hayden's 2006 RCV was totally different to the other bikes basically as an answer to the work that had been going on at Yamaha. Honda always had trouble getting their V5 into corners well, if you remember the begining in 02 Rossi was backing it in everywhere, so Yamaha exploited this with a bike that got into corners extremely well, allowing Rossi to get in front of the Honda's even if they could post a better lap time than him. HRC stole the idea, they made the motor taller but shorter with an all new gearbox and a clutch designed specifically for smooth corner entry then put a new chassis on with an extra long swingarm. It also had different fairings. The result was a bike that was much slower down the straight and not quite as quick on an ultimate laptime, but it could get much closer to what the Yamaha was doing.
it was the first bike to be raced featuring Honda's mass centralization theory,
I'm pretty sure the original V5 was the start of the mass centralisation thing, it was part of the reason they chose the V5 layout. Also why they made the bike so compact, to the extent the Rossi had to demand they made it bigger because he felt he didn't fit.