I think for Ridley, Dixie Kong, and Black Shadow/de-cloned Ganondorf, I would like for the Project M team to hold off on making roster decisions until we see what happens with Smash 4 in regards to those characters.
Project M is basically a mod to make what Brawl should have been (being as deep as Melee, but far more balanced, having Mewtwo and Roy, etc.) The five slots should go to characters that SHOULD be in Smash Bros. but for whatever Sakurai's whims were for Smash 4, were passed on.
Isaac is a good candidate to choose for this reason.
With Ridley, Sakurai could end up de-confirming him at any point. He has thrown the Smash Bros. fanbase into a tizzy ever since the first Pyrosphere update, where Sakurai made a cryptic comment that an enemy from Samus's past could appear at any moment (the area of the Pyrosphere where you fight in in Smash 4 is where you fought Ridley in Other M). Sakurai has since been either teasing or trolling (its hard to tell with Sakurai) with the Pyrosphere since then, even dedicating an entire update with a picture of simply a very large hole on the Pyrosphere where Ridley theoretically could fly in through.
With Dixie Kong and de-cloned Ganondorf, it may end up that we don't know until the game's release as to whether those two characters will be in. Sakurai has already overhauled characters like Bowser and Pit in Smash 4, so its not unlikely that he would overhaul Ganondorf, the one character for whom there has been the largest clamor to be changed up.
Basically, what I am saying is, that it would be for the best if the Project M team did not immediately decide all the slots. Sure they probably want to finish the entire project a few months after Smash 4's release (which is likely going to be Q4 2014), however, this is an incredibly rare opportunity to finally to see the long dashed dreams of the Smash Bros. fanbase finally realized if Sakurai again does not follow through on them with Smash 4 (notably Ridley and a decloned Ganondorf).