If the system were being designed today, such a design probably would be rejected as unfair. Part of the problem is that the Framers were dealing with a less lopsided distribution. The ratio between most populous state and least populous stat in 1789 was about 7 to 1. Today, the ratio between California and Wyoming population is 50 to 1.
But the Senate made sense to the Framers in 1787 for a particular reason. At that time, all 13 former colonies were like independent nations or independent countries. They could mint their own coins, print their own money, and conduct international diplomacy directly with other nations. There are lots of reasons this was unsatisfactory. It produced economic chaos and a poor prospect of winning future wars, but it did give each state the status of a country.
Now, imagine you’re a small state like New Hampshire. Right now, you completely control your own destiny. Why do you want to join a Union unless you’re guaranteed a strong voice in that Union? Now, all the arguments that people still have about the Electoral College (“The big states would push all the little states around!”) actually do apply.
It is the Senate that does a superb job… if anything TOO good a job… of protecting “small states rights.” You can argue that it is an unfair system, and it probably is… but the point is this: In 1787, the question of how to get small states like New Hampshire to join this new Union, which was after all seemed like a risky experiment, was a big problem.
It’s really for political reasons, not absolute fairness, that the Senate was created in such a way as to give equal representation to each state. It seemed necessary in 1787. But there were lots of things that could not be foreseen, such as the rise of a strong national culture and the eventually lopsided ratios between the most populous and least populous states.
Now, let me address the “House of Representatives” question. How can the Senate be based on 2-senators-per-state while the House is based on population?
