Here are my (mostly half baked) thoughts on the payments protocol proposal.

My first observation is that the proposal is too heavily oriented around a merchant/customer interaction.  I think it's equally important to consider the person to person scenarios.  It would be very cool if people could send/receive payments by copying and pasting stuff on facebook or email (you can kind of do it now, but it's not safe unless you go to extraordinary lengths using PGP signatures and the like).

Protobufs vs JSON: Protobufs are fine, although I will mention that the serialization/JOSE arguments are irrelevant...you only need that if you need a reliable way of signing an in memory object structure...in this case you would be signing a serialized form of the object...the recipient doesn't have to be able to reproduce the serialized form, they only need to verify the signature on the already serialized bytes...I see protobufs as a good serialization format for storage, while JSON being more practical for communications in a web oriented environment...with protobufs & a web wallet, you may find yourself in a situation needing to parse a protobuf message in a web browser...the protobuf parsing and serializing code is just going to add bloat to the web page...personally, I probably would have gone with JSON, but hey, I'm not writing the code.

X.509 - nasty, but maybe ok ...as long as you can add root CAs to your Bitcoin client or explicitly trust a certificate, I don't see that it poses any privacy issues...but there are some other things to think about here ...like what about the casual user that wants to create a payment request to send to their friend over email (wrapped in a clear text block similar to PGP...it could also be sent as a file attachment)?  Are you now requiring them to go and setup a certificate?  Btw, I really like the use of a payment request in this manner because you have a signed payment request that can be verified against an address book of known identities.  This could be much safer than simply emailing an unsigned bitcoin address around.

Refund addresses...this is not going to be as useful as people might think...most refunds that bitpay needs to process happen days or even months after the initial purchase...in that span of time, people can change wallets, rendering such a refund address useless...so, as I think about the situation, we would still need to contact the buyer to confirm a refund address anyway.  What we really need is to verify the identity of the person we're potentially sending the refund to...we need a way of determining that the person we're sending the refund to is the same person that paid the original invoice.  Bitcoin addresses are identities, but they are too low level.  HD wallets come to mind...the top level or intermediate levels of a deterministic hierarchy could be used for identity purposes...but it also seems like it might be conflating payments and identity (which for many reasons you might want to keep separate).  What if bitcoin clients could manage one or more identities used for the purpose of communications?  You could have a bitcoin identity file that could be used by multiple wallets.  These identities would be used for signing messages and verifying the authenticity of communications...when sending a payment, instead of a refund address, you would include one of these identities which could later be used to confirm a refund address.  In fact, the refund would be processed by the buyer generating another payment request message signed by the identity used in the original payment.  

People would understand that their identities are important for communications and they would keep those even when changing to new wallets and such (identities could be stored in ~/.bitcoin/id or something (encrypted of course)).

There are some other interesting possibilities if messaging and identities are done right...for example, I could add "check" feature (analogous to paper checks).  It would work like this...you create a transaction that spends to a newly generated address...you put that transaction, along with the private key into an encrypted container (sent to the identity of the person you want to pay).  The recipient can open it and their wallet would go ahead and generate and broadcast a transaction moving the funds into their wallet (optionally including a fee).  But, if the recipient never cashes the check, the sender could pull those funds back after a certain period of time.  This also eliminates the possibility of accidentally sending the funds to the wrong address (or an old address) and the bitcoins being forever lost...the recipient can sweep the transaction into any wallet of their choice.

As I'm writing this, I'm beginning to wonder if the identity management problem is unavoidable.  Maybe that needs to be dealt with first.  It would enable so many other interesting possibilities.

I like the use of merchant_data...this means that you no longer will need a unique bitcoin address for every invoice.

In the signed invoice structure, why embed the serialized invoice?  Why not make that a reference using a hash?  Generally speaking, I'm not a fan of embedding things like that.  You could have an over-arching structure called Message which is just "repeated bytes objects" (in protobuf lingo) ...references between objects would use a hash and the first object would be treated as the message.  In a payment request message, the SignedPaymentRequest would be the first object, the PaymentRequest the second.

I think the Payment structure should refer to the SignedPaymentRequest (by its hash) instead of the merchant_data...you can of course access the merchant_data through the SignedPaymentRequest.  I suppose you could always index payment requests based on the merchant_data, but it just seems cleaner to refer back the the signed payment request when sending a payment.

You might want to include an optional memo for each output...I could imagine including one output that says "Don't forget to tip your waiter"...any amount sent to that address could go directly to the waiter's wallet.

What about payments from multiple wallets?  We see this a lot.  I think this scheme would handle it ok, but just want to mention it.  I can imagine someone paying first from one wallet, then the invoice webpage updates with a clickable link to a new PaymentRequest for the remaining amount.

The Receipt should be signed...it could be used as proof of payment by wallets.

Finally, I've seen seen suggestions to tack on a payment request URI to the current bitcoin: URI for backward compatibility...I say no.  A bitcoin URI already has a lot of data (especially if it includes a memo)...this makes QR codes more dense and hence more difficult to scan...I say we stake a claim on the "pay" URI .... pay:https://somewhere.com/payment/94kd83  ...or for a clickable link, you could embed it right on the web page, eliminating the need for a second https request... pay:data:<PaymentRequestMessage>  ...and finally, to further shorten the URI, https could be assumed if the protocol is omitted ... pay:somewhere.com/payment/94kd83

We can deal with backward compatibility by including a link on invoices to display an old style bitcoin payment address.