How about making due dilligence easier when you KNOW there is a probable change required (ie: the need to add a plugin line to maintain default bahaviour that didn't require such a line in the previous release(s)).
At the end of make install or some reasonable place, run a scan of init.pre, or xxx.pre(s) if that method is adopted, and generate a checklist of all of the loadplugin lines found, and compare that to the default manifest for the current release. Then spit out some text stating that "loadplugin (this,that,theother)" is required to maintain the default XXX functionality from the previous release. You should add that line to init.pre if you want this functionality." You could also spit out lines to the effect of "loadplugin(whozis) references a removed plugin and will now crash your startup. You should consider removing the line from init.pre." I suppose you could even add a twenty-questions session to let the user y/n the things he would want to change, and then the script could dick with init/pre for him based on the answers. BTW, adding a "dontloadplugin" keyword might be a good thing. You could use this to nop-out old plugins. The user could use this to explicitly state he doesn't want a plugin loaded, and then at the next upgrade there is no question of "did he remove it deliberately, or did we add it and he wasn't aware of it?"