Back then the cartridges were rather large, and giving popular titles like Pokémon unique colours was good for identifying them. Now they're all smaller cards, basically, and with rising costs of everything, changing a production line to create special coloured cartridges would be an extra unnecessary cost that increases the price of the games to where some people no longer can afford them. They will stay plain grey.
I would love for them to bring back the colored cartridges for the Pokemon games, but given how not even HGSS had their own specialized cartridges, I can't see it happening :< The next best thing is the specialized box colors, but the US gets plain old ones, orz