True. It's not like we've always wanted breakaways to succeed. Often, the opposite has been the case. Then we have been talking about what could be done to make the GC riders win more stages.
It's not contradictory. Things change. And the Tour should adapt to that.
So they should make it harder for the GC leader to win the polka dot jersey, they should change the criteria of the young riders jersey (preferrably abolish it), they should remove the bonus seconds on mountain tops (as you mention), and they should put in more KoM points on the flatter stages to avoid stages with no breakaway attempts.