Crawd, I'm afraid I just don't find your definition of a Low Skill a very useful one.
The whole idea of the "Low Skills" is this: Is it acceptable to use this skill against the Emperor?
Yes, it is certainly dishonorable to use Stealth to sneak up on the Emperor. It is also horribly dishonorable to use Kenjutsu to take a whack at him with your sword, Horsemanship to ride your Utaku steed into his throne room uninvited, Hunting to track and snare his pet peacocks, Poetry to write mean haiku about him, or Ikebana to artfully stick a flower arrangement up his nose. Almost no skill is ever "acceptable to use against the Emperor," so this rule is no help at all in making useful distinctions.
A more useful definition---in the sense of helps us make specific in/out determinations about which skills belong in this group --is "skills which will never be required to discharge the duties of an honorable samurai or law-abiding heimin," i.e. stuff you would only know if you've been up to no good.
Does Stealth have a perfectly acceptable use as part of an honorable and law-abiding life? Yeah. Is that, in fact, the use of Stealth I see being rolled close to 90% of the time? Yeah. Insisting that the whole thing needs to be a Low Skill (for any reason other than Tradition! ) is like insisting Sincerity be a Low Skill because it includes Deceit. Just mark certain less-used Emphases (Ambush, Spell Casting, etc) as Low or Dishonorable, and you're good.
As for Temptation and Intimidation being emphases instead of their own Skills, I feel like it's grouping up two Skills that are already large that it may cause Courtier skill being too strong. Right now, Intimidation is used for bullying, torture and controling (control as being a longterm usage like caging someone and breaking his mind after months/years of mistreatments). Seduction is more about about seduction and bribery. Courtier is about discussion manipulation, rhetoric and gossips. By combining all of these, I feel like it's a "One Skill To Rule Them All" Skills.
If you read the OP attentively, you'll see that it already addresses this. Gossip, negotiation, and rhetoric are broken off into a different skill--Politics--along with Bureaucracy and a few other things. The focus of Courtier is narrowed to influencing people through personal interaction. Right now Bayushi Courtiers have Courtier (Gossip) and Temptation in their school skill list (but not actually, I'll point out, Intimidation); under this revision presumably they'd have Courtier (Temptation) and Politics, or else Politics (Gossip) and Courtier. Easy peasy.
First of all, I'll agree with you, the definition of Low Skill wasn't good at all. It's a skill that "... represent deplorable crafts and practices that no honorable soul would even imagine taking up." (4th ed) or, from the 3rd, a skill "... are seen as unclean and dishonorable."
I mostly focus on Stealth, what's the main usage of that skill? Let's look at the emphases: ambush, shadowing, sneaking and Spellcasting. This is for both 3rd and 4th edition. Sure there's 2 obvious reasons to not lose honor which is for hunting and scouting. Since there's some emphasis changes why not simply remove these from Stealth? Take out the "Hunting" use inside the... let's say... Hunting Skill, which already exist in the Bugei Skill. For the scouting use, how about in a new Bugei Skill: "Scouting" with emphases like trapping etc. I know they set up traps in hunting but it could be in a skill for scouts. Of course that's a suggestion, which leaves Stealth a defined Low Skill usages.
As for the "Less-used emphases" argument, it mostly depend on your games. Most of the time, in my games, people rarely uses Stealth in their "Non-Low Skill" reasons. I'll admit that my group rarely needs to scouts for a military engagement or rarely wants to go hunting. Which ends up a situational point of view. From what I'm thinking, your experiences seem different where there's a lot of scouting or hunting. Then someone could come up with a group where they almost only play bandits or assassins etc where it's way more obvious that Stealth is a Low Skill. It's like you're saying with the Sincerity where someone could say it should be a Low Skill because they are only using it for the emphase of deceit. I think it's easier to manage these few exceptions than managing the whole Skills because there's a few good way. By setting it as a Bugei Skill, you'll have to track every act that involves ambushing a Samurai, shadowing a Courtier, sneaking up a Magistrate, Spellcasting secretly in a Court, etc. Yes, the line between Bugei and Low Skills is pretty much near the middle of the Skill, but it needed a decision between both.
I think it's correct as it is because it prevents someone who isn't too familiar with the Bushido to badly use the skill. I think it's easier to know that sneaking is a dishonor if it's in the Low Skill than in a Bugei Skill. Of course, that's not dumb proof, here's an example: in my very first game, where I barely know anything about the game, one of the player, who was playing a Lion's Pride started to use seduction to convince the NPC to give him some information. Knowing that was a Low Skill and the fact that Lion was a Clan that priorise Honor a lot, I know that was a very wrong move from his character! Why? Because I knew that Seduction was a Low Skill, if it was a Bugei, I would probably just have laughed and thought it was ok. I feel like it's more a way to help the new player to understand the way of the Bushido.
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Now for the Temptation and Intimidation, yes, I've missed that, my bad. However, it feels wierd to have a High Skill with that much "Count as Low Skill".