I'm wondering, is it possible to install the 3.3.2 version of the WST plug-ins standalone, without all the other (org.eclipse.jst, org.eclipse.jpt) plug-ins? i.e. is there a wst-runtime-3.3.2.zip or something analogous?
You're better off selecting the features you want from the Update Site and installing them. The kind of separation you're seeking can come naturally from what you choose to install. Artificially imposing a separation like you're asking for doesn't serve a purpose beyond having that separation.
IBM Emerging Technologies