Developing in separate applications is the ultimate in separation of code, I suppose, but I still don't see any benefit--you're going to need to do extra work to get those applications communicating with each other without really any benefit from developing them separately as plugins and combining them to work together later.
-- Wanting separation of the code for development purposes was mostly what I gathered from the original post, and developing with separate plugins doesn't do any worse a job at that than developing it with separate applications.
The obvious benefit with plugins, of course, is that down the road you can change up which applications your plugins are in. Maybe you initially put all of the plugins in your main installation, and eventually you find that there's just too much going in there--no problem! It would be as simple as moving a plugin directory to a new app and you've got that same functionality elsewhere.
You can't quite get that level of flexibility without utilizing Cake's wonderful Plugin architecture, which are themselves much like a self-contained applications, but with a lot of flexibility and reusability.
Ben
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