I agree, we need some records that prove that we hold our stock in listed assets. When trading shares (that is real shares), I use an online broker who immediately generates a PDF when I make a purchase or sale. It usually has details such as; amount of shares I purchased/sold, amount in $, company, date/time etc. All the info you could need. I believe Bitfunder, BTC-TC and any other notable exchanges should have a somewhat similar system, so that a pdf of the trade could be provided under trade history or something. Again, I don't know how expensive or efficient it would be to set up something like that.
I can make PDF's that look like broker trade receipts. What does holding a PDF prove?
You have to trust your broker. This is not unlike btct.co where you have to trust the issuer. They get complete lists mailed to them regularly. So the "who has what" problem is solved. The other problem of trusting the issuer still exists. If you don't think you can trust the issuer, do not buy the issue.
Colored coins are great, they solve the same problem our lists solve, but they do nothing for the problem of trust. So on both points it's a wash. What they DO add is distributed trading. Conversely what they take away is a backed-up easy to use safe place to trade. Now you lose your wallet.dat (or get it stolen, it's not like bitcoind can use 2FA.) and you lose all your shares. Awesome.