In my writing I have a tendency to excessively use enclosing marks (parentheses, square brackets, and curly brackets mainly, but also double quotes and single quotes [really matching apostrophes]--dashes should probably also be included in the list, though a dash enclosure can terminate with another termination mark [e.g., period, closing parenthesis]).
This seems to come partially from a self-conceit issue, which presents my thoughts as being less worthy (and so deserving the de-emphasis of parentheses--don't attack me for making stupid comments) and raises doubts about the clarity of my expression (so that explanatory notes are appended in parentheses--don't attack me for being unclear and don't attack me for stating what only an imbecile would not know). Another motivation seems to be a desire to indicate that the content is not essential (whether explanatory [including adding details] or speculative [which might include adding variants])--sometimes being important content (e.g., content without which later statements would be very difficult to understand) which is "subservient" to the non-enclosed content (somewhat like nested lists in html).
While I have sometimes been able to reduce the number of parenthetical comments, it is difficult to do so because the enclosures provide a sense of structure and (I perhaps irrationally hope) allow a communication of details without excessively disrupting the flow--the reader could scan more quickly over the enclosed comment. In some cases, extended parenthetical comments can be broken off into new paragraphs (paragraph breaks do indicate a transition but do not indicate the "subservience" of the material).
While sidenotes, footnotes, and endnotes can provide some of this functionality, the composition tools and presentation tools do not seem to support ease of composition and ease of reading. This is particularly problematic in the presence of even limited media independence. In part because of the lack of excellent navigating tools, sizing html pages to match the functionality of pages in printed media (such that footnotes could be used) would be inappropriate. Even limited layout independence makes presenting notes at the bottom of a view port very difficult (and, in the case of longer notes within a small view port, the note might not fit in the same view port as the text that references it). A reasonable compromise might be the use of a separate, bordered block after each paragraph containing note marks.
Notes also have the issue that there does not appear to be a standard syntax for note marks. Although numeric marks are sometimes used to indicate references (which usually are suitable for endnotes) while asterisks, daggers, and double-daggers indicate comments, there does not appear to be a convention for indicating significance, length of the note, or nature of the note (explanatory, side comment, extension--even references can vary in nature, some being primarily crediting of ideas and some being more about extended explanation or context [and a reference might include an extended quote, which would not be suitable for inclusion in the flow of the text, followed by a reference to the source]). Traditional notes also do not provide a context for the note; a note might apply to a word or term, a phrase, a clause, a sentence, a paragraph or even a larger section of text (though an unreferenced endnote would probably be appropriate for notes relating to a whole section). For shorter contexts, highlighting the context seems reasonable (and the nature and strength of the highlighting could be used to indicate additional information about the link), but even weakly highlighting larger contexts would be distracting (an alternative might be to use a sidenote-like marking, perhaps a vertical bar, though I think that might not be helpful).
Anyway, a significant problem with extensive use of enclosing marks is that nesting urges a means to distinguish levels of nesting. While I commonly use the sequence parenthesis, square bracket, curly bracket (and, if necessary--though this usually indicates a need to reformat--, back to parenthesis), this has the significant problem that square bracket can be used with special semantics (e.g., to indicate a quoted mistake [sic]--which really is an inferior marking because it does not indicate the context or nature of the error nor does it guard against the error being altered in transcription).
A similar problem arises with quotation marks. Sometimes quotation marks are used to indicate approximately used or nonce terms, but that can introduce confusion for short quotations. Likewise nesting of quotations and similar enclosing marks can be difficult.
Obviously, I should reduce my use of parenthesis, particularly with respect to guarding statements. Yet there remains an issue of communicating the importance, relevance/context, and nature of statements. Parentheses also provide a better visual clue of separation than commas, which may make parsing easier (particularly for short comments). In more casual writing such as a blog or forum post, there is less incentive to rework the text to maximize readability; but even in a more formal composition (especially when there is not a length limit to constrain content) there is a place for "inline notes".
Perhaps a better but impractical mechanism would be to use styling to conditionally hide content. The reader would choose the style and the user agent would hide, include, use inline or "near-line" revealable/hidable notes, and other presentation methods to present the content of interest to the reader. E.g., the desired degree of detail, the knowledge base of the reader, the interest of the reader in side comments, or even more complex factors like reputation of the writer among peers, with the reader or the reader's trusted group on the topic--such factors could be used to tailor the presentation of a text to provide a better reading experience. (A side issue with revealing and hiding notes is that such breaks the visual recognition of the reader. The layout of text seems to give powerful visual clues to readers which allow scanning a previously read text very quickly. While text search tools can remove some of the need for such, there remains some difficulty when the reader cannot remember a precise phrasing or worse in terms of automated search if the reader only remembers that there was an interesting comment in the text or a portion of the text.)
In reading academic papers, even such niceties as indicating if the reader has read a particular reference--or a similar version--or an earlier paper on the same basic idea and including any quick notes the reader may have attached to the work. Likewise bibliographies and notes on authors could be useful in filtering and directing interest in references.
It seems that there should be a better mechanism of communicating (though a large fraction of my poor communication practices come from lack of effort), but I do not know how the presentation of text (and so its composition) can be substantially improved without extraordinary effort from the writer (or the reader).