Some would argue that it would slow down the legislative process. But looking at the sheer size of the US Code, I would argue that it's not at all a bad thing.
I'm afraid you'd probably need a constitutional amendment for that. And it might not be easier than the "getting money out of politics" one (https://wolf-pac.com/the_solution/).
As for your link, I can't even figure out what their proposed text is.
In fact, they tend to accuse California of being worse than the federal government, but also at the specific things that they attribute to the lack of a single subject rule.
We do have a sort-of example to follow in the Byrd rule, which limits what can be done/attached to reconciliation bills specifically.
Both major parties in the US benefit from maintaining the status quo. Neither one wants to do anything that takes power away from Congress and puts it back in the hands of the people.
Whichever party is in power during any given cycle is the one that benefits from gerrymandering, omnibus bills, fillibusters, etc. So why would they change something that's useful for them?
Then when the pendulum swings to the other side of the aisle, the situation still holds true. Party A and Party B will fight each other to the death, but neither one wants a Party C to rise to prominence.
Edit: alternatively, just don't allow bills that do more than one thing.