The federal constitution says that voting is left up to the states, so arguably the centralization problem is ~50 different experiments which have all gone wrong in the exact same way.
You could say that the federal constitution should have put some guidance in place to stop exactly this correlated failure, but ironically that would introduce more centralization as there would be one rule forced on all the individual states.
Whether that's a good idea or not I think depends on how good the rule is in practice. Unfortunately the rule you suggest highlights just how difficult it is to write a good one. For example, how do you define "coordinated organization"?
If both major parties split into 50 different organizations that all happened to endorse the same candidate for president (but for nominally different state-specific reasons), should the SCOTUS have the power to ban those political organizations (and perhaps ban one and not the other)?
Fortunately we can look to other countries that have managed to avoid political duopoly by using voting systems which don't penalize people for voting for new parties. Even better, some US states have already implemented such a system[0], and, going back to your point about constitutions, the people of Maine managed to introduce RCV not because of a constitutional requirement, but despite a narrow (state) constitutional prohibition.[1]
[0] https://en.wikipedia.org/wiki/Ranked-choice_voting_in_the_Un...
[1] https://en.wikipedia.org/wiki/Ranked-choice_voting_in_the_Un...