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This is probably the single most wanted feature on soup (imho):
Reactions even by people not subscribed to soup.
Also, the possibility not to show the reaction as a post. I'm not reacting to anything (and I really wish to) because of this. A comment is no way a post by itself (it could be, actually, and that's why there should be the choice).
On the one hand I do like the non-verbal character of many soups. On the other hand the comment system really is non-intuitive and hard to use:
1) Reactions "pollute" my main soup
Only in rare cases I actually want that, so the usual workaround is to create a closed group - "[mainsoupname]-comments.soup.io" seems to be a sensible convention - only for comments. Works for me, but does misuse the group idea somewhat...
2) Comments appear in mysterious places :)
Comments only appear on the original post they are directly associated with. There's no way to comment on a re(-re-re...-re)post. Even worse, comments to reactions only appear on the reaction. So you'd have to click through all the comments to see the next level of reactions. While it works for short dialogues, it's really hard to follow otherwise.
The complete thread of comments should appear on the original post as well as all reposts, together with soup specific settings for visibility. Each soup could have an automatic "virtual" companion soup for comments with another set of visibility/privacy options.
Waiting to see what the next big soup iteration 'soup.me' has to offer :).