I suggest EU4 implement a "shepherd" policy of colonisation. Colonisation would be determined by:
1. The placing of player "markers" that determine whether or not an area will be colonised by them at all. Similar to a national focus, but a few more of them, costlier, and instead of progressing colonisation they merely permit it.
2. Push factors influenced by the overall state of the player's (and the AI's) realm. Stability, religious differences, economic conditions, war, etc. all "push" migrants out of their nation and into the colonies that the player (and the AI) designate with "markers".
3. Pull factors influenced by the area being colonised. Life rating, economic gain, distance, etc. make some places more appealling than others, and can impose a ceiling on how many migrants relocate there.
That's the best proposition I've EVER read so far in my crusade to get rid of the present colonial system that dates back to EU3's release. Please powers that be, please hear him ! You could also influence the push factor by subsidizing the emigration of valid men or women like France did when they ''exported'' members of the female gender into the French West Indies and in New France starting in the late 1650s to the early 1670s. It could even be enabled by a National Idea.
That way, you could slow down the colonial process, make relationships with Amerindians a key feature of colonization, raise the cost of colonizing, make colonial wars a lot more important and also remove the micro management of constant clicking...