I really like the idea of having [title] resolved to ID number at "post" time and ambiguities prompting a list, though I'm sure this would need to be optional to avoid becoming annoying for some situations and some people. My idea of this is having "Submit" and "Preview" do this, placing the modified HTMLish into the text box, so a subsequent "Submit" or "New" will have the ID numbers. Ambiguities would show as radio buttons under the text area. So if you don't want to use this feature, just ignore it and don't resubmit. But I understand this could be some work so I won't expect it soon. A radio button for "quote the [ and ]" (making it not a link), would be nice, especially when no match is found.
But even more than that, I really, really like replacing the current "Re: Re: Re: Re:" with "Re02.01.03: " for the third reply to the first reply to the second reply to the original question. In the rare cases of more than 99 replies, a third digit would be prepended which would mess up the sorting order unless extra work was done (which I wouldn't consider worth it).
Then, once we have that, the "In reply to:" links would be done so that "Re02.01.03: Hi" is "In reply to: [Re][02.][01: Hi]" where "01: Hi" is the regular "parent" link, "02." is a link to "Re02: Hi" ("grandparent"), and "Re" is a link to the original question ("Hi"). I'm constantly jumping to a new node and deciding I'd like to jump up the hierarchy three steps but dislike the extra clicks and pauses required.
The rest of the options I either didn't like, didn't understand, or didn't really care one way or the other about.
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