I disagree with this suggestion.
Each time a waypoint is finished you need to wait for a mage to show up to open the next waypoint - and that mage also needs to have one of the 3 badges needed to open that waypoint. I fear that this will make it harder to finish all stages in time and get all the rewards. And it will make it harder to ensure that all members get a chance to donate a badge to each stage such that they can get all the rewards. Some members are not able to play multiple times a day, and with this suggestion they may not be able to donate a badge even if they have one of each badge in inventory!
Furthermore I usually tell everyone to donate a single badge off path if needed to get the stage rewards as I prefer losing a few badges this way if this means more members get the rewards. This will not be possible with this suggestion unless all waypoints are opened by donating a single badge to all of them - but this would mean even more lost badges.
If this is implemented then I will have to consider if I need to make all members mages during the FA such that they can donate badges. But this would also mean that everyone can pull the flag, so I risk the flag is pulled too early before everyone has had a fair chance to donate a badg
(Not to mention that everyone can now invite members, kick members,... but I assume this won't be a problem...)
Your suggestion would probably mean less badges wasted in the wrong waypoints (I say probably cause mages can make mistakes too and donate to the wrong waypoints) - but I think a lot more badges would be lost cause they sit in inventory when the FA is over cause the member couldn't donate them.