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!
Can I play Pokémon3D with a controller?
Yes, when you connected an XBOX 360 controller (or a controller that identifies itself as an XBOX 360 controller) to your computer, the game automatically detects it and you can play with it.
PS3 or other controller:
However, if you have another controller (a PS3 one for example), you should visit this thread and watch the video to make it work with Pokémon3D, since no other controller apart from the XBOX 360 one are natively supported: