Hi Gunnar,
I like this proposal very much - and I dislike it at the same time a bit. I probably like it more than I dislike it. ;-)
It's very easy to change the default values of the preferences, and we do this already e.g. by defining the default-perspective of a package. It's possible and it is easy. And yes, you are absolutely right that EPP is probably the best place to define the defaults for end-users, much better than Platform or CDT or any upstream project.
One thing that I like to bring up here is that I prefer to have a common look and feel for all packages. That does not mean that there's no room for deviation for single packages, but there must be good reasons.
In case of auto-refresh I'd say it makes sense to enable this in all packages. But the problem will arise when we are going to discuss settings such as line-numbers. 50% of our users hate us for not enabling this by default [1], 50% of our users would hate us if we enable it... (don't cite the percentages... it's just an example, but the message behind them should be clear).
[1]
http://www.ihateeclipse.com/
Thanks,
Markus