I don't really like the idea of appending the XML to the end of an iNES file though. I'd rather see it in a zip along with one file per ROM. Having stuff in a zip keeps it open to being able to put other things in as well such as those ADPCM speech synth ROMs, should they ever get dumped or just the recordings of them like we have now.

I want to agree with this. The old iNES format should have no influence on this new strategy. The rom data should be left alone so that it doesn't take elaborate tools and detection schemes to document and verify roms. Most dumpers that I know have moved completely in favor of DAT files. They're easily modifiable and viewable for dumpers and users alike, but they can't ignore subjective, appended data like headers. And as this new format will prove, they really shouldn't have to.