Thank you all for your comments & suggestions. I wanted to provide a few additional details and answers to your questions.
The notification system was built as a way to aggregate all of a member's subscribed content, and to indicate - in one place - where activity is occurring. It works in conjuction with the e-mail notifications that are currently sent out.
As Carl pointed out, there are two components to each notification: the author (which links to the profile) and the notification content, which links to the specific comment or answer.
The "new-notification" highlight disappears after the list is viewed, but the notifications remain in your list
I very much see this is a first-version of a notification system and we will definitely be making improvements over time.
We very intentionally created an airy, lighter feel to this version of MaplePrimes. That said, there are some areas that can be improved to reduce scrolling, and we will look at making some refinements.
Thanks again for your comments!