There's all sorts of fun to try and use the web site model. Many have tried and most have failed :) You may get some things working but plugins might not. See:
Fredrick Tjarnberg's blog post
I might be wrong, but as I understand it the reason for plugins being a problem is because when EPiServer starts it uses reflection to check the assemblies in the BIN folder to look for classes marked with the plugin attribute (or inheriting from the plugin base class). With a web site project, you cannot control the method or deployment of the assemblies and so you have no way of knowing if EPiServer will find them to iterate them in its plugin search.
Another option might be to develop your plugin in a separate assembly and deploy that but keep the rest of your website as the web site project model.