Primary development for Pokémon 3D has been passed to a new team of developers. You can view their work in the game's GitHub repo, found here: here.
Also Nintento of America Inc. sent a DMCA takedown notice to Gamejolt (where this game was hosted) and asked them to remove all games related to Nintendo's work. Read the full DMCA here.
But you can still download the latest version of the game here!