There are three things about the Senate that differentiated it from the House:
1) The biggest and most important difference was that its members were intended to be beholden to the States directly, not to the people directly. But, the 17th Amendment eliminated that difference, making Senate members directly accountable to the people like the House. I think the Progressives knew that this would not benefit "the People" but would rather concentrate power at the national level instead of at the State level. Call it the stupid American voter, but they were able to pull it off. It almost makes no sense to have a bicameral national legislature after the 17th Amendment was passed. We should repeal it.
2) The filibuster...but note that this is not a Constitutional limitation on the Senate, as Harry Reid correctly noted. The filibuster remains at the mercy of a simple majority, and can be set aside at any time. Only civility keeps part of it in place, which means it is on borrowed time.
3) Because the Senate's members are selected at the state level, and not the city level like the House, the Senate acts as a balance against urban excesses.
So, with 1 eliminated, 2 at half strength (at best), and 3 at full strength (but the weakest difference), the Senate is half as useful as it was when the Constitution was drafted. That is probably reason enough to keep the Senate de-merged from the House. But, any way you slice it, the Progressives removed a weight bearing beam from the structure of the United States Constitutional government house.