Hi! ;-)
First of all, sorry if my english sounds bad because I'm a brazilian and I speak and mainly I think in portuguese... 8-P But I understand perfectly the english language...
Here are my suggestions...
Let me say that I downloaded everything from this site.... with the exception of the guides...
1 - Split or Divide the Maps, Mods, Scripts and Guides section, one for the Cube Engine and one for the SauerBraten engine, because many people here could want to download only maps for Cube or only for SauerBraten...
2 - Create a standard file naming system (SFNS)... because I found many *.RAR and other extensions like *.cgz and *.ogz (cube and sauerbraten maps)
3 - About the SNFS mentioned above something like get the *.RAR files, unpack and pack with ZIP and the same goes to the other files
4 - The same SNFS goes to the scripts/guides and mods...
5 - When I downloaded everything one of the boring things that I found was the pages of the files (16 total) with 158 files carrying about 10 each...