Finally i have free time to read your thesis. My comment, thoughts & question :
1. On 1 - Introduction. You forget to mention 2 proposals (which published before date before of your thesis) which aim to improve anonymity which are BIP 151 and 156, even though it's not anonymization by modify transaction.
Remember that these are confined to the network layer of Bitcoin:
1. With BIP156, your IP address will no longer be tied to your personal transactions from the perspective of connected Bitcoin nodes.
2. With BIP151, all relayed transaction data will be encrypted from the perspective of someone analysing internet traffic (but connected Bitcoin nodes will still see the transactions unencrypted).
Neither of those BIPs will change the ability to analyse transactions on the blockchain
2. Upcoming bitcoin proposal, Schnorr MuSig could improve privacy on transaction with multiple input, you might be interested.
No,
Musig Schnorr makes using multiple inputs less expensive. This only incentivises coinjoins, it does not make them any more private.
edit: Musig is for threshold based multisig that is safe to use with signature aggregation (without Musig, the last person adding their sig to an n of n aggregated public key could cheat by throwing out all the previous keys and replacing them with 1 key that belongs to them, and pretend that all the previous people's keys are aggregated together into it, so they can steal everyone's money). And so Musig doesn't have anything to do with privacy or anonymity on the blockchain either