I've done it before, doesn't mean that it wouldn't be better as a mode. Especially in MM where I can totally see myself completing a heart container by accident.
I've been against full heart containers as a reward for defeating a boss for a while anyway.
I don't like 3 heart runs, since there are several enemies who could one-hit kill you with that (Iron Knuckles in OoT, King Bublin in Twilight Princess) and it feels so cheap. I think it would be ideal if you could only get a maximum of 10 Hearts instead of 20, while the enemies are stronger and faster.
That could be done with giving no heart containers for Bosses and needing more heart pieces to get one container.