Why the New Configured Port Wizard is confusing
It is generally known, I believe, that BizTalk has somewhat of a steep learning curve.
BizTalk server is by no means a simple product, but that's ok because we tend to do complex stuff with it :-)
Microsoft, over the years, from version to version, invested a lot in making the server easier to learn and use, some improvements were made in the UI, but mostly through investments in the documentation, tutorials, examples and "community content"; I do believe this has made BizTalk much more accessible.
There are still quite a few things in BizTalk which, from my experience, tend to confuse new starters; one of them is the concept of orchestration ports and port type and the "New Configured Port Wizard".
I find that too many developers use BizTalk without fully understanding the fact that it is a strongly typed system and without understanding the relationship between ports and port types (and messages and [multipart-]message-types).
This is not helped by the fact that you can quite easily develop an orchestration without explicitly defining either.
The new configured port wizard defaults to creating a new port type whenever you configure a port; I suspect many developers never give it a second though and simply create a type for each port they use; this way you can easily create quite a few copies of the same type and not even recognize it.
further more the wizard creates the port and the port type, but only completes the port type definition when you connect the port to a receive/send shape that has a message configured (the message-type portion); I believe this further confuses people as 1) it does not make it clear that the message type is indeed part of the port type definition (along-side the access modifier and the message exchange pattern) and 2) as the port type definition does get completed when you create the link, many developers do not understand why they cannot replace the message in the receive/send shape, or connect another receive/send shape to the recently created port (because the message types may not match).
If I had to guess I would say that the reason for the way the wizard works is the assumption that it lowers the entry barrier to developing BizTalk processes as people can develop processes without understanding the concept of types) but, in my view, here lies the problem - developers produce code they do not fully understand with all the problem that creates.