Ok.. I would love to see a relpacement set for all the paper tokens to plastic with verbal desciptors (I am old and my eyes are going.. they are very hard to read.. just me..) and separate effect and counter tokens to denote permanent effects.
Not to steal an idea from another game but I played Heroscape forever and they had effect markers on the board that possesion of (having a figure on the marker) did various things.. all puppets gain +1 def, combat, move.. sew up the puppet that lands on the marker first.. etc. You get the idea. Would make for major combat areas.
I am also tempted by different board configurations. I like the base board but find it kind of bland though with larger boards comes other issues of gameplay as this is meant to really get in close and duke it out.
Some scenario driven type games might also be interesting adding some diversity to the game (especially for multiplayer.. team based options would be nice) i.e. assault/defend point A on the board and capture/defend it in/for X turns to win.
Expansion wise I agree with the themed box release idea. Inidividual puppets would be cool but we know that isnt happening. Another option might be to 'build a box' to mix and match a custom pack of individual puppets but I guess that technically is individual sales. I would like to see new masters maybe more than new pawns personally.
The event deck concept also sounds interesting with different positive and negative effects for a turn with a new card flipped every trun not round.