Claydol used to be different colours but then in gen 5 they changed him,
his body used to be brown and his eyes used to be sort of red/orange.
Now his body is almost black and his eyes are pink.
Now I know it's because that's how GameFreak wanted but is there any other reason or possiblity?
Technically they did not change his colours, they made them a darker shade. I guess they just thought he looked better that way. It is not the first time they have changed a Pokemon's details before. Just look at Gengar:
Look at all those changes!
The only Pokemon I am aware of that they changed for a specific reason is Jynx. Jynx apparently looked like some racial stereo-type and caused a lot of problems for nintendo so they changed it's skin colour from black to purple.
Before After Now