Well, I think the thing is this: When the project started out, it seemed like such a nice idea. An FPGA-based recreation of a mythical and sexy Commodore computer that never saw the light of the day. With a few minor changes to the specs, to finish what Commodore started and to make things a little bit more usable.
During recent times, there was a lot of stuff added into the computer which - to me at least - seemed a bit over the top (Matrix screensaver, cough cough). It seemed a bit like the team wasn't so sure after all what the MEGA65 should become. Should it be the recreation as planned or should it be more like an Amiga or a complete fantasy product? Though I can understand that some things might evolve and change during development, I had the feeling that the goal wasn't really clear anymore, and sometimes I wasn't so sure anymore if this is really a computer that I would want to buy (whereas I was 100% sure when the project was first announced).
Now to top it all off, this new website came out of nowhere, with all those fancy phone ideas and handhelds and whatnot, and I think it should be understandable that at this point, it's possible that some people really start becoming sceptical about the whole idea and whether there is still a clear goal for the team. And those who thought the MEGA65 is mainly about recreating the C65 might have the feeling that this initial vision has been replaced by something completely else.
It might not be as dramatic in the end, but it wasn't communicated well (the site was suddenly there), and in my opinion, it would be nice to see the team sticking a little bit more to the original idea, to avoid confusion.