I think the only correct answer to slow down colonization is to increase the number of bad event compared to f.ex. native assimilation. Maybe im wrong but i seem to get positive outcomes more often the bad ones. I found this little read on the first colonies as a quick look at how perilious it actually was:
http://nationalhumanitiescenter.org/pds/amerbegin/settlement/text1/text1read.htm
Lets say all
overseas colonies had loads of horrible events where you would have to step it up and cash out either points or ducats to keep the colony alive. These could be connected to time periods too - like pre 1500 it would be hell to get a colony started - combined with the allready slow tickle of new settlers.
Making these events separate between overseas or no would stop it from affecting the f. Ex. americas, russians+ east asians too badly.