How to handle proxy caches cleanly isn't immediately obvious to me, but there's far more tools with this approach than the zip file approach. Certainly with work I think it could be solved. Again, to a first order, the proxy would have to accept this style too and do something intelligent with it; an old-style proxy would fall back on the current system.
It is not clear to me: Are you the one proposing this zip file thing, or someone in another group that is working on this? If the latter, I wouldn't mind seeing a link, perhaps even submitted to HN.
What you're saying is close to what we've been looking at trying to turn into code. I think the proxy thing is a non-issue. In fact a proxy in many ways could implement a portion of the server-side smartness and accelerate conforming clients on websites that don't implement this.
These are some larger issues though, I think:
1) Making the server smart enough to actually do this.
2) Sending the resources in the right order (It turns out the order things go down the line can be significant and this is something that can vary depending on which web rendering engine your user has.)
3) This requires changes to HTTP, unlike the linked proposal, so one needs a way to do it right and a compact representation of the cache information.
We're in the middle of a research projects right now where the server automatically constructs cache groups and does this properly. It was one of the things the guys working on spdy and us talked about, but they are taking a slightly different approach.
We'll see what happens, but this is the direction we want to move as well.