I'm guilty of indulging in scriptaculous, and I believe that, if used well, it is worth the extra downloads. I'm thinking just for AJAX comments, you could do the same thing with about 1/10th of that file (most of the effects, etc you do not use).
However for pages with more extensive use of AJAX/JS in general, the full library would be justified. Pages that, IMO, are justified for prototype (and such) are pages with many tedious fields to fill (password...) like signup forms, where the user doesn't want to wait for the page to reload to know that the username is took, or that their passwords do not match.
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