Why Directory Opus 10 is the king of file browsers
nerdbusiness.com
nerdbusiness.com
Nautilus is pretty customizable with hotkeys, ways to interact with not only Git but other VCS-es through plugins or otherwise. I appreciate you introducing Directory Opus though, I'll definitely take it for a spin on my Windows boxes.
I can however vouch for xplorer^2, both feature and speed-wise which is my default file explorer in windows.
On a substantive level, I think all file managers should have tagging, smartly filtered collections (a la itunes "smart folders", but more powerful), and built-in full-text search. On top of that, a rules engine for copying/moving around files (e.g. move all downloaded pdf's older than 15 days to the trash). Ideally, this stuff would be higher level than the file-system, thus allowing cross-platform use of this system.
Some of the features you're looking for are rather dynamic - so might be beyond the scope of a file browser. That kind of thing might take it into the realm more of a passive service. Though, in another 20+ years I can certainly see DOpus accommodating that.