As to JBDS, we can change the default value when starting a new
    workspace. This can also be done in JBoss Tools, but would break
    Eclipse fair play rule.


I don't understand why this was never a preference in Eclipse already. 
It seems to me Eclipse is being too lame to be treated fairly in this 
case. You can change just about ever other aspect of a project. Maybe 
I should voice my concern on an issue report. Is there an open issue 
in Eclipse to control this setting?

    

I haven't found any, but the issue can be easily fixed.
  

You are saying Eclipse WTP actually reads the default from a preference but it is not exposed in the preference pages ?
Then sure, lets open that up and even better submit a patch to Eclipse WTP so it becomes available in the December release of WTP 3.2 which
we will need for other reasons anyway ;)