The solution is federalism, which we already have; a Wyoming voter controls the Wyoming state government, which has power over things that are purely internal Wyoming concerns.

What incentive do rural states have to stay in the union if the federal government is controlled by populous state bullies? Wouldn't it be better for them to fragment into separate-but-open-border-countries like the EU?

Probably roughly the same incentives any state has ever had to join and remain in a federation. Things like free trade and movement among states and a combined military. One of the incentives to remain in a federation should not be the ability to disproportionately influence the federal government compared to other member states.

That's certainly fine for state-by-state issues, and it is the case for most of them, like state income tax, sales tax, most laws, etc. Unfortunately there's only one President, which is why this NPV issue concerns the presidential election and not anything else.