EDIT: Wait a sec, what if a map uses textures contained in another PAK file? Seems like if that was taken to the extreme (a map drawing from 4 or 5 different paks), it would increase load times quite a bit.
I think pak files do increase load time, but not as much as pk3/zip files, which require pre-scanning and decompression.
Since pak files are already supported, what is the purpose of this feature request? Are you suggesting all the game data be put into pak files?
-Plus then for each map it could have a map info file, the custom textures, the map, and a picture in it, so that as the game is loading, it displays a picture in the corner. (like most Q3 engine games.)
Pak files aren't necessary for any of this.
The other problem with pak files, is, say like 10 people create maps using textures from the CTP and include those textures with their map in a pak file. All of a sudden, there are 10 copies of the same textures. Then what if y00tz updates the CTP later with some texture fixes and tweaks? Which textures get used? There are 10 to choose from?