We have made the choice to focus around people and conversations rather than topics (because Lyra is designed to be harrassment-proof, and topics lead easily to harrassment - you don't see this so much in the tech world but in the mainstream it's a huge problem).
We are currently thinking about the best way to do notification aggregation (Facebook does this very badly - several comments on the same conversation will give you several different notifications) and marking-as-read. We have several interesting options in test at the moment.