Well, one nice improvement they could do is to add filters for all of the notifications. I wouldnt mind filtering certain builds off, the UP, or even entire planets. In the OP's situation, he would therefore only see notifications for EXACTLY what he is looking for. Without filters, notifications on big games are nearly useless, with all of the clutter.
Speaking of notifications, how about a notification when you have birthing rates enabled, and you hit max pop!?!?!?