So they could agree to pass two bills. This would require the two "sides" to trust each other, but it could (ideally would) also function to build trust, which would be a good thing.
Assuming there was enough trust to "guarantee" that one bill would pass right after the other, then what's the point of having the single subject rule in the first place? Sounds like you still have riders but with extra steps (and an opportunity to betray trust).
Because it becomes harder to "hide" things - like, the provisions being bargained for, or politicians' actual convictions about particular measures. There are items which now get passed in omnibus bills, bargained for behind closed doors by leadership, which couldn't (whip votes as ye may) be passed in up-or-down votes on their own merits. Those are, in my opinion, corrupt bargains, and shouldn't happen. I like legislative horse-trading - it's an important part of the democratic process - but I'd like it to be open and above board.
