The collision is probably one of the weaker points, I agree. The problem is trying to simulate round objects with hitboxes and pixel maps - which are, by nature, not round. I didn't really have the time or knowledge to extend Flashpunk's collision engine to support circular bodies, so the marbles are represented by a square, and the holes by a circular pixel map (with jagged edges, because pixels).
One feature I would have liked to add would be a slight acceleration towards the centre of a hole when you get close enough. That way, if you are travelling fast enough, you could skim around the edge of a hole.