I would say the biggest problem with desktop notifications right now is that there is no indication of what I am being notified about.
A notification can indicate a new like, a new comment, a community post, a new pledge - and when I click the notification icon to view them, there’s no indication which is new because they aren’t sorted by newness, they are sorted by category and date. Even at low activity levels it can confusing to remember which notification was the last you looked at in any category - “oh I have 3 more comments and a new pledge, but it said I have 6 notifications, were the other 2 just likes?”
There is no sorting mechanism to just look at everything new that has happened since your last visit or clearly see what those new notifications are, and there’s also no filtering mechanism to turn off notifications for things like “likes” that aren’t really that important.
I think a simple way to fix this would be to ask yourself “why should I click on the notification icon, what am I expecting?” - For me I click it so I can see what’s happened since I last came to my patreon page, and unfortunately, it doesn’t fulfill that role because it’s not ordered or marked in a way that I can easily see that.