Suzu Fanatic

In my experience, there's an exception for the hyphenization-of-honorifics rule when the original Japanese would add a glottal stop. When this happens, it's usually represented using consonant doubling. For a non-translated but salient example, the weeb visual novel Katawa Shoujo uses both "Shicchan"* and "Hicchan" for Shizune and Hisao respectively. For something the old guard will get, look at poor Sacchin in Tsukihime. The same applies to stuff like "Takkun".
*a Hepburn hardliner may argue that this should be "Shitchan", but fuck them, I only write "matcha" for green tea because normies use that spelling).
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You might want to either linebreak the document manually or use something else than github or, idk, change some setting; lines are currently not automatically word wrapped and reading the text online is thus a pain. I had to copy it to notepad++ to read it personally.
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The "other sometimes untranslated terms" heading is confusing when it comes to terminology. On first reading, it seemed to me that you were placing "senpai, sensei, onee-san" in the "not honorifics" bucket, especially since you end with "bento" which actually isn't one. On second reading I realized that you may not have meant this, but it's a mental stretch. I think this section needs to be rewritten.
I think the correct heuristic, if you keep any Japanese words, is probability of comprehension. The most common honorifics that people may know about is -san, -kun, -chan, and -sama. -tan, maybe. Knowing about "nii-san" and "nee-san" comes next and is somewhat more dubious, and those terms arguably carry more important information that you may be denying uncomprehending viewers if they are not clued in by other details. "senpai" and "sensei" are slightly further out, but not much. All in all I agree with the position of removing honorifics, however.
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This ideological statement needs statistical backing. From what I understand the people you consulted with have been editors, not readers, and honestly preferring to reverse name order is status signalling by people who consider themselves more "learned". For what it's worth, back when I was a nascent VN reader I was bothered by the reversed name order used for the localization of Ever17.
Since  what you're really trying to do is establish standards, removing the ideological statement and letting the rest remain is also fine.
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I disagree with your interpretation of "Uuu" -> "Aww"; the mapping is simply too imprecise and will cause conflicts when lazy people decide to apply the letter of your guideline. For example, part of one line in the wondrously transliterated Koirizo fan translation is rendered as "Uuu, gusu" in its English translation. Gusu is a sob, Uuu is a sound of consternation and unhappiness in this case. Writing this as "Aww, sniff" would not accurately portray the tone the VA used here. I might be mistaken about how Americans interpret "Aww", however - I see it as 1. dejection 2. disappointment and 3. you just saw a kitten do something cute.
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Despite what I said about ideology above, I would like some kind of justification for this, hedged unless you have good reasons not to. Reading the comment thread you have done so in the thread, and considering that you made personal remarks further on in the document, you may want to add it for this.
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You could make some fairly strong demographic arguments as to why this is a good idea if you wanted to. I guess you might have left it out for a reason, though.