Why should some be national? Not every Civ can Colonize the world. That would be odd. There were only a couple of colonizers: the Portuguese, Spanish, French, English and the Dutch. One might add Germany and the Norse, but that's really it.
Having 6 of the same colonies allowed means that only a few civs can have those luxury resources. Furthermore, this way I could build more of the same colony to get a monopoly.
Besides all that, I thought it would be really nice if you could trade colonies with other civs, like you can do with technologies. But that's maybe something for later. What do you think?
While only a few civs were major colonial powers, most of the big players had some areas on the outskirts of their empire that fit the definition of colonies. The Russian development of the Siberian Ostrogs aren't really equivalent to the Spanish conquest of Mexico, but would you argue that either didn't fit the definition of colonialism? And really, the colonial powers each did their colonizing differently; compare the Spanish model to the English and you'd have a hard time arguing that they're the same thing. The proposed national wonders are the types of colonies that everyone had access to - look how many India Companies there were, and how many countries at one point or another controlled a Carribean island full of sugar plantations.
Even some of the Muslim civs had colonial areas - look at how the Arabs spread throughout East Africa. Keep in mind, also, that you listed 7 civs as colonizers, leaving out the Russians and Arabs, in a mod that has 18. 8 or 9/18 is a pretty solid ratio - why should we cut everyone else out arbitrarily?
Not everyone can colonize the world, but there are still limited numbers of colonies to be built. Why shouldn't there be competition for them open to anyone willing to invest the resources? Why shouldn't the Romans be allowed to build the Great Wall, or the Germans the Statue of Liberty? Why should anyone other than the Russians and the Americans be allowed to build spaceships to win the game? Do we want to make the game completely deterministic, or have some flexibility built in? Not every civ will be competing on equal footing to build colonies, and some won't have the temperament, resources, or technological advancement to do it. Only a few civs, largely the ones you mentioned, will have colonial UHV requirements.
As initially proposed, colonies would grant more than one resource - for instance, Cuba might grant the builder 4 tobacco, which could then be traded to other civs. Nobody else would be able to build Cuba, and there might only be one other colony (Virginia) which would give access to tobacco. If a player built that colony as well, they would have a monopoly. This models monopoly practices and limited resources quite well, and takes the slot of some of the resource-granting wonders (Wembley, Graceland) from RFC. This reduces the learning curve for playing the mod, which is also one of our explicitly stated goals.
I don't see any way of making colonies a tradeable commodity. Trading cities, which is pretty close in intent, is essentially impossible with civ and RFC AI. As written, colonies are projects rather than geographic places - there's no way to make them transferrable between one place and another.