It doesn't mean that bitcoin is "not designed for micro-payments"... He merely clarified what would happen to certain transactions if txn fee is not included. Remember, the goal is to eventually have fees assigned to pretty much every transaction in the block chain.
Stating that fees will be required for pretty much every transaction in the blockchain (and basing the value of those fees on the size of the transaction in bytes) pretty much implies that bitcoin is not "designed for micro-payments", since the direct effect of micro-payments in the bitcoin design is to result in very large transactions (in terms of bytes) for a very low value transfer. As such, the transaction fee becomes a prohibitively large percentage of the transaction value.