I understand English-speaking countries have most experience with colonialism, but there were plenty of other kinds of imperialism and subjugation (and slavery and mass murder). In the end it doesn't matter if the guy enslaving you and killing your family is the same race and lives 500 km from you or a different race and lives 3000 km from you. That was history for thousands of years. Almost all countries started that way.
Slavery is called so because Romans took Slavic people as slaves. Are we supposed not to make games about Roman Empire? And to change the name of a whole linguistic group?
I don't think changing the setting from historic to sci-fi or fantasy suddenly makes exploiting goblins or genociding elves OK. And if Porto Rico is bad then so is Risk and chess (and 99% of all board games that have aggressive war as a core mechanic).
I don't think games have colonialism problem as much as "war is the easiest mechanic to make fun" problem. And I don't think morality has anything to do with this. It's exactly as moral to make a game about killing human race with a deadly virus as a game about colonialism. But I'd prefer if we had more board games where conflict isn't military - simply because it's been done too many times and it's boring.