To me the current state of the art (visual art & animation) in 2D adventure games is Machinarium. It has plenty of subtle animation, which I find sorely lacking or of poor quality in much of 2D games.

To answer this question properly, you'd have to conduct interview with Amanita Design on what strengths and issues they found in using Flash to make their games (Samorost 1-3, Botanicula, Machinarium). That would be interesting read as I don't think I've seen one that digs in how much help or hindrance using Flash really is.