I like David Baron's alternative to X-UA-Compatible: if the main problem is intranets, give intranet folks a way to configure IE to use the old rendering mode just for their hosts.
I'm interested if this would be enough for Microsoft. If they claim it does not cover all the cases, it would be good to get some sort of metric/percentage of how much it would cover. Seems like it would cover the vast majority case. Probably close to 100% of the cases where Microsoft's revenue is impacted.
If the claim is that they cannot "break the web" even for that small case on the internet where their revenue is not directly impacted, I wonder how important those sites are anyway. I expect there are lots of sites that were made with older browsers in mind, but the site is probably abandoned too. As long as you can sort of read the content on the page, maintaining precise layout is probably not important.
If Microsoft is still set on using a flag/switch in HTML/HTTP header, I still prefer a cultural flag and not a product version flag.