To get an idea of why I use WAP over WSP I'll point you to an article I wrote about this a while back. WAP or WSP Which to Use and Why.

Michael Washington wrote  Ryno wrote   Has anybody made a WAP tutorial that is as good as the WSP one I posted that covers using Visual Studio 2005/SQL Server 2005?  I have one here: http://www.adefwebserver.com/DotNetNukeHELP/DNN4_WAP/ but it's short. All my other code including the code I do at work is WSP. The reason all my samples are in WSP it was the only format that worked with Visual Web Developer Express. Now that will change with the new asp.net service pac. However I will continue to use WSP because I simply prefer it at this point. Some prefeer WAP format but If you like WSP continue to use it because the final result is the same as far as the asp.net runtime is concerned.

While I prefer WAP, I was going to mention...if I had started with WSP back in the day, I'de probably stick with that. 

Deploying modules in either WAP or WSP requires some thinking-through on the steps, including prep and test time for the installer.  While I find module dev using WSP very-strange, it's probably only because I'm so much more comfortable with the strangeness that is WAP module dev.

Ryno wrote I guess this discussion begs two questions.  First, why are there two different PA models?  Secondly, has anybody made a script to convert one type to another?

There are two PA models because Microsoft has created two compilation types. There is no converter that I am aware of.

Honestly the reason I prefer WSP model is because people can simply install my code and easily open it and modify it. I put out a lot of code into the community every week. I can see how that is unusual. For an private developer I can see how this simply would not be an issue.