Definitely the Supremes overreached in Baker v. Carr and the other state apportionment cases.
In the Great Compromise, the members of the Constitutional Convention agreed that each state, no matter how big or small, would have two members in the U.S. Senate, while the House would be apportioned based on the population of the states. updated every decade through the Census. It was a sensible solution that (notwithstanding recent problems with the filibuster, senatorial holds, hyperpartisanship etc.) has worked out pretty well, all in all, over the years. So what if there were state senate districts drawn along county lines, rather than being based on population as most if not all lower state houses were? States copy some of their structures of governance from the Federal government, and vice-versa. If voters in State X don’t like having their state senate districts drawn along county lines, or heavily favoring rural voters at the expense of urban voters, they can either (1) prevail upon their legislators to redraw the lines, (2) pass a state constitutional amendment to do so, or (3) sue in state court to protect their rights under the state constitution. Sooner or later any or all of these would almost certainly have led to a just result, and without the Supremes meddling in very localized forms of governance.
I agree with the great majority of the Warren Court rulings, but I have to say I think they bungled this one.