My understanding is: Chrome splits popups into two categories: ones triggered by anchor elements, and ones triggered by other JS. The ones triggered by anchor elements are assumed to be useful and are not blocked. The ones triggered by other JS are hidden and placed in the titlebar.
So the theory is that advertising popups would fall into the latter category, and functional ones into the former - but it seems in practice, sites which want to show popups actually just have them be created every time you click a link and don't bother with creating ones without clicks, since they are always blocked. So you still end up getting a lot of popups getting through the blocker.
My proposal is to eliminate distinction between the categories, and just block all popups. It's rare to come across a site which uses popups legitimately, and even in that case most of them are not triggering the popup on click so the popup is being blocked by the current policy anyway.
EDIT: Although, someone just pointed out a very common legitimate usage - Oauth / facebook login. Guess this is a tricky policy area.