The main problem with the DALY is that it's not intuitive, combining so much that an estimate can be off by 100x without anyone noticing for years.

That was not the conclusion I reached when I read that post. If you want to write something arguing for that claim, I'd be interested to read it, but it seems to me that there is a much simpler explanation that people just don't care enough about saving lives or years to bother to do calculations correctly. They are only interested in justifying the programs they are already attached to. I suppose you could say that the very idea of quantifying charity is unintuitive, but this doesn't distinguish DALYs from the Other Dave's criticism of "lives saved."

Edit: For example, a widely quoted Peter Unger footnote is off by 3 orders of magnitude. But he never asks himself how Unicef is able to save a billion lives each year.