I have written about this before on the forum and spoken directly to Michael about. I think its a good idea to bring it up in the forums again to see what others have to say.
I pointed out a while ago that a certain other CMS whose name I shall not mention, but it begins with Word and ends with Press, now has an automatic update system, as its core functionality is separate from content - as it should be. Michael said that this would be introduced in Pulse and it has been.
But personally I have had no luck with it. Most hosts do not allow PHP uploads of the size that Pulse has become. .htaccess settings can sometimes overide the server restrictions though.
Last time I experimented with it all content files were also overwitten. The time after that it looked like it was going to work and then just stopped.
So, as I am happy enough working directly with files and FTP this is the way I now do it.
Download and keep a copy of pulsecore/storage as well as template and content folders.
Then nuke and pave.
Afterwards upload my saved copies of the essential folders.
Couple of issues here: I feel that the storage folder could maybe be placed outside of pulsecore to make things more simple. Also as I have just upgraded a live site to 5.3.2 and broken it in the process - there is now some disconnect between content and core functions. It took a while to figure out what was going on.
For instance, the blog has changed so that the code on your pages also has to be altered. In my case it was the titles that went missing. They now have to be added as a separate tag.
This is actually a really good change and will allow more versatility in the way blogs can work.
However it cannot be done automatically because its part of content folder. Therefore this kind of thing needs to be better documented in release notes - specifically how to upgrade!
Same thing with layout.php - slight changes there.
There may be others that I have not spotted too.
Its a great system and also a work in progress, so this is not a whinge as such, more of a suggestion really. We all want it to succeed and be the CMS that we can use.