Fungibility (or lack of it, not sure about how to use the term tbh) what can be done? I don't like the idea of using some Bitcoins that were once used by some criminals or something. With cash this is not a problem because we don't have a public ledger for cash, all cash is the same, but with Bitcoin, all transactions are recorded for everyone to see. I know confidential transactions are coming which is cool, because its no one's business to know how much money you are moving but you and the other party, but ultimately this does not solve the fungibility problem. So how do you keep the ledger public, while making it impossible to know if your Bitcoins are "good bitcoins" or "bad bitcoins" so to speak, so all Bitcoins are the same? There is already a market for "freshly mined bitcoins with 0 transactions": see this
https://blog.blocktrail.com/2015/07/announcing-blocktrail-mint-fresh-bitcoin-delivered-from-the-mines/I think everyone deserves the same level of anonymity and fungibility, no matter if you are expert, noob, wealthy or poor. It shouldn't be something "extra". I hope this makes any sense.
The solution is not Confidential Transactions alone. The ultimate solution is the combination of Ring Signatures with confidential transactions and is under development
There is no reason why bitcoin could not duplicate this work in a side chain. The advantages and disadvantages of side chains of course is another discussion. The point is that the changes you request are too drastic to ever be implemented in bitcoin itself.