Seems like a solid enhancement. Though, unless something is done to make the clickable notification bubble visually distinct from other notification bubbles to provide some sort of positive indication that it is clickable, likely to be an enhancement only known to those who already know about it (and anyone who finds it by accident). Given the minimal style of the admin menu, this could be potentially difficult to do without making things look cluttered.

A more immediately usable option could be to add an "Upgrades" link to the Plugins submenu when there are upgrades available (And "Pending" to Comments, etc). This still saves the extra click, plus it doesn't require an UI retooling.