I don't understand why the <aside> semantic can't be applied to footnotes. The HTML5 draft currently suggests using <a> links, but this does not properly set the semantics, and does not also allow alternate rendering for footnotes, notably between paged media, aural media, and non-paged visual media.
The links also does not allow setting properly the relations between groups of footnotes with document sections.

Why can't <aside> element include some properties to suggest the intended location, such as after the section end and before the next section, or at end of the current page, or at end of another higher-level section (such as the current chapter, or current book), or below the current paragraph or block (the smallest section level), or by default beside it (if possible, otherwise it could become another block possibly rendered with indentation (by default), or a frame around it (the effective style for the note's block could be defined also by a stylesheet).

Using the title="" attribute is also bad from a pure accessibility point of view (it won't work properly for pages medias, notably when printing, where another visible location would be preferable, with the same additional grouping semantics)

I then suggest extending <aside> to offer:
- an identifier for the side/foot note : this would be the visible number, or typographic symbol used to access the note from the text where it is referenced, and that would also be automatically inserted at the begining of the note's content. Aural medias may need to change this identifier. Optionally, this identifier could also be a number, generated automatically, according to the notes numbering rules in the group of notes to which it is added.
- a notes grouping mode (or an automatically computed group according to some rules, such as a set of sub-section levels, generally identified by its heading type like chapter, book) which describes how far the note will be located from the main content section where the note is inserted.
- some rendering hints (probably part of CSS styles) for various media types (notably for visual paged and non-paged medias)

And then to deprecate, from a semantics perspective, but also from an accessibility perspective, the legacy use of the title attribute, or of links.
Instead, <aside> notes will just be used to define the content of the note, and there will be a way to insert a reference to it within the main content, where a visible link could be automatically inserted according to the <aside> element properties and its associated CSS styles.