It's a fickle problem. I think the only real solution to this is to go by the character's base form and perhaps do separate articles for the different forms, should they exist as MUGEN characters. That does mean Goku would need to be split into Goku and Super Saiyan Goku.
As the person who sorted out the categories on the Kirby page (and a lot of other Nintendo character pages) I would like to chip in and say that the category system is a giant mess that I have been trying to clean up.
All of the categories on that page were put there because they are technically correct, seeing as we have no actual documentation in relation to categories and I was merely working off of what seemed the most logical solution; the Mega Man category is similar in the technicalities of what weapons and elemental powers he uses in his source games (due to my unfamiliarity with the series, a good hour was spent trying to datamine the Mega Man Knowledge Base).
The problem that arises with the base form limitation is the question of 'what qualifies as the character's base form?' Kirby may only be a Wind Element User in his source game base form, but what about Smash Bros. where he's also a Hammer user (side-b), Sword User (up-b, final smash) and an Ice Element User (custom regular-b) in his base form?