On rebooting the lore of L5R, I feel that the most important part is making sure that it is internally consistent. For instance, some stories I have read seem to indicate that Rokugan is very large, while others (such as many of the stories of courtly intrigue) only make sense to me if Rokugan is small. Making it clear that Rokugan is the size it needs to be for a particular story might work, but some people might find it annoying. I don't have much history with the game, so I don't have any desire to reboot to the Clan Wars.
I would approve of a person's honour being controlled by the people around them, but this would be overly complicated if each player had to record how the clans see them. Perhaps the PCs could have a shared honour score that shows how the groups they have come into contact with view them, which would mostly be whether they like or dislike the PCs.
On the Reboot - that's why I think a reboot to something close to the Clan Wars is desirable. I really believe that the clans in the their current state are not reflective of their original intent. They've changed over time as a result of card mechanics and the outcome of tournaments, not because it is necessarily "appropriate" or "on theme" to have a story go in a particular way. While I think that having a meta-plot in a CCG is a cool idea, I don't know how faithful an RPG should be to that premise. I know there's a desire to see the two as "linked" and taking place in the same current universe - unless the RPG writers are constantly doing meta-plot updates simultaneous with the card game story-line that's a really difficult design philosophy to stick to. Though, to be fair, I have always been MUCH more a fan of the RPG than the card game which may explain my reluctance to embrace the change and also why I feel like I don't really lose anything if the story reverts. I don't have a relationship to it.
I'm not even saying it needs to go back to the "canonical" time of the clan wars - just to some time that a) is not dependent upon a deep understand of over 2 decades of CCG lore and b) presents the themes of the clan in a "pure" state such that they can easily be communicated to new players and will be recognized by players who maybe have been away for a little while but are coming back for the new edition and designers.
As for the honor discussion:
I actually think that this could be tied into the court mechanics somehow. As some people on these forums have stated, I agree with the idea that there should be a "micro" as well as a "macro" game for courtly politics. The way I ran my court games was always in "seasons" with each season taking place at a different court or at two geographically close courts. While it could mean extra book-keeping I think that the courtly exploits of the characters could be tracked at the level of these various courts. While there maybe dozens of possibilities I think that only a handful need to be fully detailed out by the designers - so long as some guidance is given on how to generate and track things like influence, glory, favors, and yes even perceptions of honor as to the character in that court.
Regardless though, I also think that there should be an individual component to honor as well - I just don't know what that should look like. Maybe bonus dice depending on your character acting in a way that emphasizes a Bushido virtue in which he is particularly strong? Free raises? If roll & keep is not maintained - this could be something else entirely.