Hi!
Back to the topic of the Cloned Tiles UI:
One issue is if you try to apply one of the non-rectangular wallpaper groups to rectangular prototype, the result does not appear to make sense.
Showing schemes like http://thorwil.files.wordpress.com/2010/08/wallpaper_groups1.png would help a bit. But actually, the user should start with the right shape. They should be encouraged and assisted to do so.
The "Use saved size and position of the tile feature" allows one to deal with geometry that extends outwards of the base tile, as nicely explained on http://tavmjong.free.fr/INKSCAPE/MANUAL/html/TilePattern.html
I think this is a hack to seemingly get around the need for 2 different things: the base tile area used for building the pattern (gap-less, no overlap), and the prototype with the geometry to be repeated.
A solution could be to put this functionality into a tool/effect. You choose the Wallpaper group, then you create the base tile area that will have the right shape (similar to rectangle/star/polygon tools). There could be automatic selection of geometry covered by the base tile area. If you start with a selection, the base tile area could be created centered on it, automatically.