If I understand correctly, there are two methods to perform a multi-signature transactions in Bitcoin. One is "pay to pub key hash", which is a method commonly used to send standard single signature transactions. The other is "pay to script hash", as specified in BIP 16.
If you use "Pay to pub key hash" , any senders to the multisig address need to specify all the public keys involved in the multisig address, which can be cumbersome. If you use "pay to script hash" , the sender only needs to know the hash of the script , which is equivalent to the length of a single bitcoin address. Obviously, "pay to script hash" fits better with the various infrastructure already setup around the standard transaction.
Are there any other advantages or disadvantages between the two methods?