The cap on the size of the House should be lifted, so that an approximately equal number of people are represented by each representative, no matter what state you live in. I don't see the problem in both California and Wyoming getting two senators, since that's (as you mention) precisely the point of the Senate.

It's very deliberately built in to the American political system that the will of the half-plus-one majority does not dictate the direction of the whole country. If anything, the ever-increasing Federalization of laws and policies is the real problem: Californians living like Californians is fine, and Wyomingites living like Wyomingites is also fine, but there is a problem when one tries to make the other live more like them.

Let's have fifty vibrant laboratories of democracy.

> how many presidential elections we can go where the "winner" receives fewer votes than the "loser" before people seriously question what the purpose of our democracy is.

I'm already questioning that myself, considering roughly half of all eligible voters don't even bother to show up for presidential elections -- let alone midterms, which is more like two thirds. If we consider that chunk that does not vote as being OK with the status quo, then I think we have a lot of room left before American democracy is really imperiled.