We, the pokemon3d.net staff, has from now (2016-09-02) discontinued work on this project and handed it over to a group of volunteers on Github. The project will be open source, and you can help develop it from now on. Check out the repo here.
"Why?" you might ask. We have unfortunatly lost interest in continuing development on Pokémon 3D. 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!
Why does Pokémon X not learn move Y at level Z or through breeding?
We are currently in the process of updating every Pokémon's move-set to Generation VI, but doing so slowly. Breeding moves are currently semi-implemented right now partly because their priority is semi-low, but rest assured, they will be implemented eventually.