Just some ideas here.
Wiki pages will be stored as XHTML documents. Pages are rendered to HTML (and cached as such). The client can then be sent Wiki Markup (XHTML->Wiki Markup) or some sort of semantically markup-ed HTML (XHTML->XHTML). Client can send back Wiki Markup (Wiki Markup->XHTML) or semantically marked-up XHTML (XHTML->XHTML).
A module should be developed that does the two directions of conversion.
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Internal representation of a wiki page as a certain style of an XHTML document.
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Plugins (out) this internal representation to wiki markup, XHTML (rendered).
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Plugins (in) turn wiki markup, XHTML into internal representation.
Stage 1
Get the GUI editor working well with normal hackish wiki markup to HTML converter code.
Stage 2
Do the stuff on this page. This step can be skipped, actually.
Stage 3
Wiki markup will need to be supported as long as many devices can't effectively use the rich text editing features. Or at least until the point at which the downsides to editing HTML are greatly over-shown by the advantages of developing for a just-rich-text environment.
At this point we'll ditch wiki markup entirely, instead just storing some kind of XHTML.