The problem with the US Senate isn't so much that it's malapportioned, in a federation upper houses are generally designed that way because federations exist where there's sub national units of diverse sizes and dispositions and a political system has to cater to that. For example, North Rhine Westphalia has 1 seat per 3m people, Bremen has one per 200k. Tasmania has 1 seat per 46k, New South Wales 1 per 700k. México state 1 per 6m, Baja California Sur 1 per 290k. Sikkim has 1 per 600k, Uttar Pradesh has 1 per 8m.
Once you've decided to have a federation and a bicameral system, it's not really unusual or unfair to have a chamber that represents the federated polities. Hell in some systems the members of the upper house directly represent the legislatures of the states etc.
The bigger issue I think is that there's no proportional representation. In most federations that have proper upper houses (ie not Canada lol) there's a good degree of party diversity in the upper house with multiple parties getting elected at once in each state, or at least in most states in the case of India. It's rare for a single party, including a governing party, to fully control the chamber, which makes it work better as a house of review.
Even putting aside that a bunch of US states are just rectangles made up to vote about slavery, I think the biggest issue in the US is each Senate race is just for one seat. That's just replicating the terrible FPTP system in the lower house over and over again rather than providing a real source of diversity and review. Double the size of the chamber and elect all 4 senators in each state at once and you likely start to get much better representation including a more realistic chance for other parties to hit a 20% quota for a seat. Go to 600 senators and 1500 House of Reps seats and things really start to look more interesting.