What needs to happen, and I believe devs are already aware of this, is to add discrimination that comes from pops, rather than from the government. All of the laws that we currently have in-game are strictly about discrimination coming from the state. But as we all know, even if the state doesn't discriminate, the people do.
So even on multiculturalism discrimination still needs to happen.
Racial and cultural tensions between pops should definitely be a thing, as a drawback to the society being so diverse.
I think the underlying problem is confusing discrimination with separatism. "Discrimination" in game terms refers to a minority POP, who has no separatist desires, becoming radical due to laws which limit his civil rights based on religion, race, or ethnicity. (Also, trying to quantify discrimination will turn the game into a war-crimes simulator.) Imagine, for example, a Sephardic Jew living in 1836 England? What legal changes does he want?
Since he is not a separatist, he doesn't want to establish some sort of Neo-Judea in Great Britain. Rather, he wants to be free from legal discrimination. He wants to have the right to vote, serve on juries, be elected to parliament and so on. In other words, he wants separation of church & state and multiculturalism. If he is radicalized by private discrimination, what is his solution? Either he demand more laws protecting him (Anti-Discrimination laws), or he could become a separatist and attempt to establish a Neo-Judea in Britain. The later course of action is absurd. Demanding anti-discrimination laws just moves the in-game problem of multi-culturalism over another step.
However, nationalism and separatism aren't caused by discrimination, low standards of living, and the like. Rather, separatism is fundamentally driven by nationalism. The separatist isn't driven by grievances, but by a desire to live an ethno-state of his own liking, and impose his language and customs upon others.
The underlying factor is ideological legitimacy, and such legitimacy is only tangentially related to the ability of a system to provide good government. The legitimacy of the system can fall with standard-of-living crashes, loss of wars and other national humiliation, and so on, as the promises made by the current system are refuted. But the underlying source of legitimacy is ideological, rather than practical.
However, that being said, I don't know how to implement such a system in-game. Realistically, the Poles, Hungarians, Serbs, Irish, etc should be demanding independence just because. But, such a game wouldn't be fun the play because the player would be stuck with radicals that exist just because. Vic 2 did sort of try to show that realistically. For example, if you take a state, the "rightful" owner will forever be declaring war on you if they think they can win. However, even in that game, there were work-arounds for the player. If you were a high-ranking great power, diplomatic incidents due to separatist movements were slowed down.