I'm inclined to agree with the Capcom Euro guy here, really the point of the Dev Room was to let the fans decide about most of the game features, characters, etc. The Reaverbot boss design contest was like that, too; it was up to the fans to design the boss fight and boss design. They were essentially asking the fans to co-develop the game with them from the get-go--it's strange that people are surprised about it now.
They did the same thing with MegaMan Battle Network 6, where I believe most if not all WWW Navi bosses were designed by fans, so in essence a large part of the MMBN6 plot was kind of built by the fans, too. The entire ClockMan scenario from Operate Shooting Star was based on the winning entry from the OSS boss design contest. I believe they were trying to do the same thing here, putting the game together from the community's best ideas, except on a much larger scale. And they can't do that if only 15,000 or so people sign up for their dev forums, even though the MML3 Dev Room has been all over the internet, having been featured on all major video game news websites such as Kotaku and GameSpot, and all the while the major Mega Man fan sites like Protodude and TMMN were constantly rallying people to sign up for the Dev Room. If despite all those efforts, only a handful of people (relatively) show up, it's not strange that the higher-ups think there's too little demand.
That said, I do agree they made a major mistake in delaying (and eventually not releasing) the Prototype Version as it would've been a good cash grab for them (wasn't it almost finished?) and it would have been the best way to gauge interest. Heck, they could've just slapped some multiplayer features on it and put it up for sale as a full game then expand on it with some DLC maybe since that should be easy to produce at this point.
All in all, it's a troubling turn of events for the Blue Bomber, now the last upcoming Mega Man game that isn't a Korean MMO has slipped off the radar...