Really, all this backroom talk is nuts - bring on the direct popular vote for President and transform the Commission into some kind of Senate that we are directly electing as well.
You seem to be under the illusion that the Union is some sort of democratic project. Backroom talk is the foundation on which its existence stands on. The Parliament is only there to give some sort democratic credentials and not actually wield any real power, and considering what sorts of results we get in those elections, it's not something that anyone sane actually wants to change. Commissioner Le Pen, that'd be one for the history books.
Also, the commission is the executive branch of the EU, so it would be strange to make that the Senate. Council of Minister would be the the more obvious parallel I think.