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 can I not log into GameJolt despite having the latest version available?
The message explains it pretty well: if you get this message and you already have the latest version, then the game is about to be updated. GameJolt needs to be updated before the game because of security reasons, so you just need to wait for the next version to be released before you can log onto GameJolt again.