Naively it seems to me that when editing, the footnote content should be right there where the reference is. This means you can easily edit the note, and avoid hassles like orphaned notes when you copy/paste stuff, etc. e.g:
This is my sentence with [[note1::Sentences are usually more well constructed than this one.]]. Another sentence follows.
Even other paragraphs.
_,~'^'~._referenceList^'~._,~'^
Would give:
This is my sentence with note1. Another sentence follows.
Even other paragraphs.
note1: Sentences are usually more well constructed than this one.
I'm completely making up the syntax, of course (especially the reference list bit). The important part is to have separator or indicator syntax of some sort, to differentiate between an optional reference name ("note1" in the example above), so it can be referenced again from another spot with [[note1::]] and the reference content ("Sentences are ... this one.").
Optional names can default to normal footnote numbers, so [[::thanks, Obama]] will get a superscript 1 or whatever.
You might also want to allow inline-type wiki markup, maybe even block stuff:
This is my sentence with [[note1::
Sentences are usually more well constructed than this one.
]]. Another sentence follows.
Anyway.. TLDR: put footnote content inline with the reference to it.
Cheers
;Daniel