Ok, to start, I have not really looked into how to do the whole PR thing (so I know this isn't formatted correctly, etc and if there's been an issues section, I'd have posted this in it instead.)

That said, there is a major issue with the current implementation of setting up an IR remote and that is there's no easy way (that I've found) to "set and forget" the protocol. Adding one line to /system/etc/init.d/02remote takes care of that issue.

       if [ -f /boot/rc_keymap ]; then
            /vendor/bin/ir-keytable -c -w /boot/rc_keymap
+++         ir-keytable -p `head -n 1 /boot/rc_keymap|cut -d " " -f 4|tr A-Z a-z`
        fi

The first line of my rc_keymap reads "table sony, type: SONY" so it now sets the protocol to sony at boot. Most of the supplied keymaps have UNKNOWN and for those, this change wouldn't do/affect anything (ir-keytable will simply thor an error message and move on.) Without some method of changing the protocol, it'd be stuck on the rc-6 & licr protocols.