I've been using Drupal for a while now and as a developer there are a few things I really dislike in the 6.x distributions.
Now I know most off these points are being fixed within the 7.x distribution; I'm still wondering what I could do in order to make those frustrations go away. The Drush, Simpletest integration with Windows can be fixed by using cygwin and it's possible to install those quality measurement modules like coder yourself. And surely it's not to hard to create a multisite environment with a core drupal installation within a VCS like perforce. There're several solutions out there that will make it possible for you to export a Drupal Website Definition to a dump file, which can be imported within a clean Drupal Install. So yes, I can circumvent those five nuisances ... but that still means a lot of work in order for a sysadmin.
At least for the jQuery part there's no real solution, for it seems it ain't possible to register the "external" js or css dependancies you have. It would be great when the Drupal Guys could provide us with such a feature when they launch number 7.x.