First of all:
I LOVE this map generator ! And I am really looking forward to a stand-alone / desktop version of this ! *excitement* 

My questions:
Is it going to be possible to import custom cell grids to the MFCG ? Like the ones generated by Azgaar's Fantasy Map Generator for example ? Or any other cell grid created via vectors ? As far as I got it your algorithm works with generated cells and fills them with content - which can be exported into svg-files.
I was thinking about the other way - importing svg-files to the MFCG, filling those custom shaped cells with city content. Probably doesn't work with curved lines ? Polygons only, hm ?

Anyway, you did a great job on the MFCG ! I love it :)