It was a bad idea necessary to bribe the small states into joining to keep the colonies together in a time with more important issues. The EC's population bias was also intentional, it doesn't make it not fundamentally undemocratic.
And the admission of states has always been very political. They have been often admitted in pairs to maintain political parity of the time and other proposed states (the state of Sequoyah) were rejected for political reasons (balancing east-west states or just racism, you decide). There's a reason statehood for Puerto Rico, a territory with more than enough people and no historical impediments like DC, isn't just a formality of waiting for a request by its people.
The Founding Fathers made a quite good first draft for modern democracy, but they weren't oracles and they made compromises based on the political needs of the day. There's a reason we don't install American democracy in countries we regime-change.