James,
the anonymity of the Bitcoin network is not entirely what you portray it to be. Data mining techniques can help to reveal the identity of the participants. See http://arxiv.org/abs/1107.4524. However, it is possible to build substitutes or different forms of Bitcoin that increase anonymity. One example would be the http://bitcoinlaundry.com/. Also, physical forms of Bitcoin, such as Bitbills or Casascius coin essentially allow the same anonymity as you have with cash.
Apart from the predictable supply, the main advantage, in my opinion, of Bitcoin, is the decentralised open source nature. It is much more difficult for third parties to interfere with the usage (compared to current banking system and remittance services), and easier to use it for innovative services.
I don’t think you can create an online anonymisation service with physical commodities as base, because I don’t think it can be decentralised, and it requires substitutes to work (unless you can figure out how to construct Star-Trek-style transporters). Due to its centralised nature, if the issuer is shut down, the digital currency becomes impossible to use (as that requires the issuer’s servers to be online).
I’ll even skip the whole issue of regulation (banks and digital backed currencies are regulated, Bitcoin is not). And even if there was a regulation that inhibits the use of Bitcoin, it’s unclear to how it would be enforced.
Bitcoin does not require substitutes to add new features (it’s possible, and sometimes advantageous, but not necessary). With precious metals, the only new feature you can add is to coin it. Everything else (e.g. bank notes/warehouse receipts, bank accounts/wire transfers, cheques, debit cards etc) is a substitute. Substitutes cause all sort of issues, like the Austrian favourite complaint, fractional reserve banking.
It is a complex topic. In some areas, Bitcoin has a comparative advantage, in others it does not.