(by design! the point was to give smaller states a say and that itself is the problem, it is a bad idea to let a minority be able to grind all action to a halt. You say "but what if they do something I don't like" and the answer is vote them out next time, elections should have consequences and winning an election should result in a government that is able to accomplish policy. Setting it up deliberately to deadlock just because they might do something you don't like is a terrible idea and needs to stop being viewed as some kind of virtue of the design of the American system. Just because the founders did it, doesn't mean that it is a good design, they had lots of bad decisions... like slavery, and setting up the government to allow slave states to have equal control to the free states.)
if you assume some kind of relative equality of states, then on the whole the senate should approximate the house, and you can easily come to the conclusion that we really don't need the senate itself at all. abolish it and go to a unicameral system.
Similarly the parliamentary system where the executive is chosen by the majority of the legislature is a much better idea - again because it results in a government that is actually able to accomplish policy.
there is very much a reason that none of the other countries whose constitutions we wrote over the years (Japan, Germany, etc) use the American system. Everyone in power realizes that the American system is terrible and doesn't produce a mandate to govern.