I have to say that I'm with Pwnemon on this one. Yeah, we hit some pretty rough patches with Mollux, and yeah, we lost some very talented contributors over its course, but that's not all bad. I think that some of the rough patches that we hit also sparked some incredibly unique and interesting discussion; I loved, for example, the in-depth discussion that we had at the beginning of the project about what exactly "bad typing" even means (I maintain mono-Normal is the worst typing). As for prominent contributors leaving, that's just a natural part of history when a project runs for as long as CAP has, and it too has its benefits, such as allowing newer contributors to be more confidant and vocal without feeling like they had to have been here for ten projects to actually be heard. Maybe I just feel like being optimistic today, but I think that there have been a lot of great things to come out of Mollux along with the regrettable, and enough people have dwelt on the regrettable, so I'm going to try to dwell on the great.
That's not to say, though, that I don't see some things that I was definitely disappointed with. On of the big ones, already mentioned in this thread by nyttyn, is the issue of people forgetting that this is a community effort and that getting your ideas "stolen" is a good thing. It means that you had a good idea, and it means that, even if it's not explicitly stated on the CAP's webpage, there's recorded text right here on the internet testifying that your contribution affected the outcome. Heck, I'm still on my high from getting so many people to "steal" Mantle as their species name in the dex entry thread.
EDIT: Oh, and because I just don't think that it can be said enough, massive props to Mos-Quitoxe for submitting such an AMAZING art design.