Between-state apportionment of power is quite a different thing than within-state constitutional amendment process. CA has a voter ballot initiative constitutional amendment process, most states do not. NC has a dual legislative & popular vote for constitutional amendments, most states do not. Within the state, all citizens should not be denied the equal protection of their laws.
The checks and balances of the federal system should be preserved. If certain large states feel they are disenfranchised by hundred-year-old-compromises, then they may seek to persuade voters to amend the constitution via the two means, or seek to form a new country with their preferred means of distributing power.