You don't really need permission...
He doesn't own Pokemon.
Do you know how many people here on Newgrounds post "fan-flashes" of Tankmen, Pico, Foamy, and many others?
As long as you gave credit where credit is due...this guy really doesn't deserve the recognition or the authority as he doesn't own Pokemon. He should be happy that someone appreciated his work so much that someone would make a flash one it.
Many examples are presented on Newgrounds all the time. So many parodies of Tankmen, Pico, Salad Fingers, Foamy, etc.
And all the artist had to do was give credit where credit was due. They didn't have to do Hours of research, blogging, and asking to Locate the original artist. A credited name is sufficient...and should've been appreciated.
Newgrounds is about creative freedom and exercising those animation skills.
Everything by Everyone.
And you took that time to give the credit...but I don't think that guy had ANY right to tell you what to do with an animation featuring characters that aren't his to begin with.