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The points you list would go a lot closer to at least making it simpler for those of us with Harmonys.
Particularly "ability to rename a remote's buttons and group several remotes together. "
Add to this the ability of importing templates of those groups - we could all help the process by submitting button layouts and groups for the various remotes - not just harmonies.
If you did go nuts and add Harmony remotes so the end user pretty much thinks it built in, I still think using an established remote config (like the Plex config) is just as ideal - it also means that when users inevitably switch to XBMC/Plex the remote support is already completely mapped in the app and ready to go.
I can understand not wanting to rely on Logitech that they don't exactly update/change current remote codes - but is this really an issue? If a new remote comes out Logitech surely adds another remote code and name - or else they would have all the same support issues when things break.
Anyway thanks for coming back on this - I really think any work on this area only makes RemoteBuddy more appealing.