Well, there are at least standards in that Ctrl-K is color, Ctrl-B is bold, etc. It may be that the colors themselves are not standard, but the use of Ctrl-K is. It may not be part of the protocol, but it's still a standard. Getting an agreement to allow/handle more colors either using Ctrl-K through 99 or using some other method among the major clients would make it possible to use more colors over IRC once the clients are updated to make use of those colors. They don't have to agree on a specific set of colors; just that they will handle more colors in a specific way.
Just a thought. I don't really expect it to happen. Though mIRC could just force it to happen considering it's a leader in IRC clients and if mIRC users suddenly started using a lot of colors, other clients would need to either block those or handle them or their users would get upset at all the numbers/codes/etc that are mixed into their text incorrectly. But I think what will happen (if anything) is just that local colors will increase, but you won't be able to send more than 16 colors to anyone else.
