The big problem with any archive format is that it then requires that you pull down the entire package, even if all you need from it is a file or two. Our repository stores files individually, which eliminates that issue -- you only ever pull exactly what you need to transition your system to the package versions you've requested. (That said, downloading multiple files has more transaction overhead; we want to download multiple files from a package as a bundle, though we were investigating MIME, I believe, for that operation. Krister will have to fill you in on that.)
The downside with zip in particular is that the table of contents is at the end of the file, which means that you can't do anything with it until you've finished downloading it. This may not be a huge issue if we depend on anything but https for security measures -- you'll want to verify the whole thing before you install it -- but it may limit streaming. Like you point out, zip has a whole lot of nice properties in terms of being a common format, but I've never understood this particular design decision. Danek
