The only real problem I see is that the colonies (be they African or Asian or Siberian or whatever) are too easy/desirable to industrialize. Historically, colonies throughout this period were seen as sources of raw materials and labor, with industrialization seen as markedly undesirable - factory outsourcing I don't think really started until after WWII.
I think three simple tweaks would help here:
a) remove the prestige bonus for turning a province into a state. When the US turned, say, Montana into a state, I doubt it really made anyone ooh and ahh in the government offices in Europe.
b) Make it harder to improve infrastructure in areas with low life rating. This is really the key. Right now it costs no more to build a railroad in the plains of northern Denmark than it does to build one across the jungles of the Congo, which makes it as profitable to build a factory in the latter as the former, and much more so once northern Denmark 'fills up'. This is a very large distortion that tilts the equation too much. I don't know if this is moddable, but I think this simple fix would help a lot.
c) lower (a lot) literacy rate gain in provinces. If African provinces had literacy rates in the teens, even later in the game (as I think would be historical) it would make it much more 'punishing' to your RP to turn them into states.
These are definitely good ideas from the perspective of limiting the industrial potential of colonies, because that really is the main issue right now.
The only thing I would tweak is your approach to the first idea of limiting the prestige benefit of forming states. Personally, I think the ease of turning colonies into states should be tailored more to individual countries. Ideally, this could be done by making it easier for certain countries to turn colonies on specific continents and with specific majority cultures into states.
For example, the U.S. should have an easier time turning North American colonies into states and an easier time turning colonies with a majority Yankee, Dixie, or Texan population into states. Russia should have an easier time turning Asian colonies into states and an easier time turning colonies with a majority Russian, Ukrainian, or Byelorussian population into states.
Basically, the scheme I have here is that a country should get a bonus for turning a colony into a state if it is on the same continent as the home country and if it has majority population of the home country's primary or accepted cultures. Colonies that do not meet such requirements should be extremely difficult (I'm thinking it should be impossible to be honest) to turn into states in the first place. Obviously, given the fast rate of assimilation in V2, it's only a partial solution, but it would still help curb rampant British Indian industrialization because they would get a major penalty to turning colonies not in Europe and not of British/Anglo-Canadian majority into states, and it would take a while for the Indian colonies to become British majority.