JS is ubiquitous because it's the only runtime that MS has ever bundled with Windows that was more or less compatible with other non-MS implementations running on non-MS platforms. It also does not utilize obfuscated and constantly changing object code formats, which is MS's forte.
> It also does not utilize obfuscated and constantly changing object code formats, which is MS's forte.
CIL is insanely simple (I've written a CIL->x86 compiler in a matter of hours) and has only had small, incremental changes since the very first version.
Are there really any examples of what you're talking about outside of the Office team?
Well, they have a spec for it, but it's not very good. That said, despite PE's history, it's remained largely the same for what, 15 years? Small changes to support various things, which make parsing arbitrary PEs a pain, but it's not bad considering its age.