"When user does check for updates, Neon.2 and Neon+1 are two update
possibility. Will p2 go down the most aggressive path that will require
remediation (removing third-party plugin that the user may not be ready
to part with) or will it try a less aggressive path that will resolve
cleanly?"
The update mechanism in Eclipse will only update automatically if it can update all existing features successfully. So if it tries to upgrade to Neon, but there is a feature that requires Mars only, it will fail the update, and instead present a dialog with some possible choices (one choice being uninstalling the feature that requires Mars-only, so that update to Neon can proceed). But it will never uninstall features automatically, or proceed with an update that breaks such features.
That's why I think it's ok to have Eclipse try to update across major Eclipse versions. If there is a 3rd party plugin that is only supposed to work on Eclipse 4.3 only, then that should be specified if the feature where the plugin is bundled with, so that Eclipse isn't broken when a major update is attempted.