Consider that, in OSGi, bundles have no concept of direct dependence between bundles.
Instead, each bundle lists the services and packages it expects to be registered by other bundles via the "Import-Package" and "Import-Service" headers.
On the opposite side, a bundle lists what services and packages it plans to export via "Export-Package" and "Export-Service". Thus, there are no hard dependencies between bundle implementations. As long as some bundle provides your imported packages your bundle will be happy.
As an illustration, WTP (Web Tools Platform) has Duplicated javax.wsdl plugins:
Now you should make sure you have converted your 3.2 Plugin project with the sub-menu "PDE tools" (right click on your project).
Then you may define an product for your rcp application, in which you will define a configuration (target) for runtime, as opposed to a development target.