Caprica was never really canon IMO. J Michael Straczynski had nothing to do with it, and it failed in no time because viewers hated it. It was covered here at GateFans (search). Besides canonical issues, the show was just too full of exposition and forced drama IMO. I hope it is decanonized. But how? I suppose if the foundations are explored again and those elements aren't there, it will be erased by ignoring it. I will look and see what happens!
JMS wasn't involved with any BSG stuff from what I know.. did you mean Moore?
CAPRICA set up the story of the Cylon Rebellion and how the Cylon Centurions and other worker models used the Human networks-- like the VR entertainment-- to communicate and organize. We also had the TPTB's squeeze in a story of the first "skin job", their daughter
a victim of the "success by accident" of BSG--which so many shows fell into the trap of like SGU. As well as having the show go too slow in some plot lines, too fast in others or just not enough detail in ones many ppl would have liked to see more of- like the Cylons themselves
the overall theme of the BSG major plot - 'all this has happened before...' was handled ok, though for anyone who didn't watch BSG, they would not have understood. From what I have read, this new show is supposed to also follow that theme, being set in our future, where we will make the same mistakes as the Humans did on Caprica, on Kobol and the other "Earth"
but, TPTBs will probably change all of that in favor of some schlock