Until we can completely separate html code from php code it will always be hard to upgrade. It may not be the easiest thing but you can always follow the code log and see what has been changed and manually make the changes on your site. For example, last night and today I fixed a few bugs and it logged the code changes. If these were .tpl (template) changes you could view the files and what were changed so you always stay up to date. You can view the log here
http://pligg.svn.sourceforge.net/vie...runk/?view=log