Drawbacks
Coordinator
In this implementation, service is a trusted server, that coordinates participants. Although the coordinator is not able to reveal the private information of the participants, it can still prevent the protocol from starting or completing.
A possible solution is to make an open, decentralized implementation of service, that can be run and trusted by anyone.
Sybil attack
Participants can collaborate in the room, to reveal the identities of other participants.
For example, if 4 of 5 participants are malicious, they can reveal the identity of the last participant, by revealing their outputs to each other.
A possible solution is to make a much larger number of participants in shuffling process, so that the probability of a such attack is very low.
The other solution is to make an unpredictable, random algorithm that will distribute participants into smaller "rooms" which will shuffle separately.
Timing attacks
The protocol implementation relies on network communication with its latencies and possible disconnections during the protocol execution. That's why one of the participants can repeatably disrupt the protocol execution, by disconnecting.
Sudoku analysis
While Coin Shuffle provides a reasonable level of privacy, users still need to be careful about not revealing their identity through their actions. For example, if the user will send his tokens to the same address from different shuffling processes, some external viewers can easily analyze the history of the transactions and participants of the recent shuffling, and reveal the identity of the user by Sudoku analysis or even just intercept inputs' and outputs' addresses of the transactions.
The only solution is to use new separate output addresses for each shuffling process.