Portugal didn't really colonized all that much in real life, the population in 1500 was something like 1 million, not enough to populate a lot of land. What it did was claim a large region, mainly Brazil and Africa, and for the most part just built forts and some cities in the best and most important places, hell, in Brazil the amazon was only truly occupied in the 1960s. That’s part of the reason Brazil is a multiracial country, they sent the men and they “acquired” the women in the region.
What I would like to see is that you could claim a colonial region, and if another nation colonizes there you gain a casus belli. If your military power is high and you declare and win the wars for the region then the AI would respect your claim, if you don't they will just laugh at your face, just like in history. Then you would slowly colonize and develop the region, a process that takes decades, sometimes centuries.