As long as all the limitations are followed and the themes are implemented, can fangames be submited?
There are a lot of "ifs" and "maybes" when it comes to using someone else's Intellectual Property that I can't really answer. As long as you don't use somebody else's assets and clearly mark where your characters come from and who they belong to, this shouldn't be a problem for the purposes of the game jam. There are no prizes this year, so you've nothing to lose by entering it!