Isn't it possable Geodude are like Humans? They come in many colors! (Dark, Tanned, white, pale) Ya know.
Then there's another possibility, maybe Geodude are like humans another way. Maybe when he's brown, it means he's getting tanned! (Like humans tan in the sun) That would explain why he went from grey, to progressivly browner. (He's more of a tan on avarage).
And to evolve, you have to battle right? So he goes out and battles in the sun turning Brown!
What I'm trying to say (Yes, I do occasionally have points somewhere in my ramblings) Geodude was greyest in his first episode, in which since brock couldn't leave his family, he probably didn't leave the inside of that gym often! So he was pale (grey). Then he joined ash, and was used in the sun more often! So he got tanned! OMG, what a lame excuse. Sorry, I've been awake to many hours in a row 'n.n
I said brown.