Apps could definitely be more modular and the recent addition of contrib.staticfiles to trunk will help greatly with, um, static files!
Templates aren't really a problem, are they? Django will find the base ones and you can overload them if you want.
settings should be handled elegantly with sensible defaults that you override if needed.
And finally - the root url config is a bit of a bottleneck as every app that has URL's needs at least an include here. A registration system would be good but there are thorny issues to do with ordering of the URLs.