I don't hate the idea of bounties, but someone has to decide what bounties to offer, and the current system for deciding that is whether money can be made in that area. It's not perfect, but at least broadly it means that there is an incentive for treatments for conditions that affect a lot of people and ones with a high cost of disease without treatment.
The thing I could see easily being missed by bounties (or maybe worse, being subject to being lobbied by pharma companies with a drug in the chamber) is drugs that start for one indication, but pivot or expand to another, and drugs that are second or third in class. There is undoubtedly some value to a second in class drug that is more efficacious and safer, and line extensions are also helpful for expanding the use of a drug in market.