I think you bring up some great ideas so I was just gonna add in my own, I was thinking of plant mutations so maybe after a plant kills a certain number of enemies then an arrow appears above their head. Player can click on this and choose from a branching tree of mutations which change it. So one might make the sunflower shoot faster, another might make it shoot stronger bullets etc. I think you can go to a lot of places with a branching evolution tree if that makes any sense.
Great game enjoyed playing it. :D