One supposed "weakness" of colored coins (I use the quotes because I personally see it as a strength), is that the bitcoin protocol doesn't verify the "amount" of colored coins transferred.  I can inspect any bitcoin output, look at its "value" field," and, provided that that TX has been mined into a block, I know that the output really contains the stated number of bitcoins.  With colored coins, this property does not exist; instead I must follow the chain of colored transactions back to the original issuance of the colored asset to determine if the (e.g.) 1,000,000 stock certificates I'm about to buy is actually valid.  This means that SPV nodes cannot verify transactions and that the whole transaction chain cannot be pruned.