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Do you mean a toggle to make pools hide posts in the index?

That might be a simplification in some ways, but I think the only case it'd really improve is #3 (pairing without hiding), which is sort of a niche case. The rest are sort of a lateral move. It could probably handle the same things, but it'd be a bunch of new UI and user education, and a lot of design questions to figure out.

For example: it'd bloat the pool list, which right now functions as a list of interesting post groups; need some mechanism for purging empty pools, eg. if a duplicate is deleted; using the "order" mechanism to indicate which is the conceptual "parent"; some equivalent of quick parenting with tag scripts.

Your final semi-issue could be resolved with a 'completed' switch for the Pool. Your viewers will know when it is ready for download.
The batch issue is that, while I don't care if people download the batch, I do prefer that people who like it to actually spend the time to use vote and/or favorite each one appropriately, which is less likely to happen if a large batch is posted at once. Staggering posts (posting 5-10 images of a set a day, say) probably helps that. It also means there's no need to hide them (there's not that many at once). I don't care if other people do or don't do this--I'm not suggesting it as policy--it's just something I try to do.

Of course, as we've talked about, score isn't everything--in fact, isn't much at all, in some cases, even range_murata is largely 0/1, wtf?--but at least that avoids making it worse.