to make it easier to compile, bring bitcoin to more platforms and attract more users it would be a good idea to use automake. I think configure options, like --disable-gui would also be easier to implement.
An other interesting thing would be some kind of standard. I think this is a very important thing for a project like this. A digital currency based on a standard is much more trustworthy (that's maybe not the correct word) even when there is only a single implementation. It also helps to be clear whot to program before starting to program. In my experience writing some kind of specification or standard first leads to better software, but that's only a personal opinion.
I know there is this paper, but what I am talking about is RFC style. The Tor people also have something like that.http://www.torproject.org/documentation.html#DesignDoc
I know, someone has to do it and the project hasn't too many developers yet, but it may be a good idea to implement them early to attract more developers.