I have a one year research project in my MSc curriculum. So i was suppose to address a existing issue in bitcoin protocol. Highly appreciate if someone can advise me and give me some ideas.
Selfish mining is probably one of the most addressed issues that was theorized by a group at Cornell university. I find this interesting, because rather than being a technical issue such as transaction malleability, it is more of a conceptual issue with how Bitcoin and its consensus system works.
That should get you started and give you some food for thought.