I could not really pinpoint why the new UI is bad, but it got me to finally switched 100% over to emails to manage all my GitHub notifications; I disabled them in the Web UI completely.

I find my email client (Thunderbird) and custom filters to be a much more powerful and flexible way to manage the hundreds of notifications I get every day. More than 99% of these emails are automatically sorted in folders, tagged, etc. So that I can efficiently prioritize what I look at. This saves me massive amounts of time. In the end I always have an empty inbox, which I find pretty satisfying and it helps me focus.