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AS2 is based on HTTP and is fairly well adopted
AS3 is FTP based but I've never once been asked to look at or implement AS3.
As far as what you setup for each partner, I would ask the partner what are their capabilities. You will find many partners are only capable of using a Value Added Network. This is a great option for most partnerships, but VAN's usually charge by kilo characters so they do have an expense associated with their service. You should poll your partners and find out what is the most common delivery method among the community. If it turns out that most are using a VAN you will be hard pressed to convince each one of them to implement a new communication protocol. Some partners may only have FTP or secure FTP. There are many ways to deliver the payload and you have to research what will allow you to connect easily with your trading partner community.
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