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I would like two have more control over how to determine fitness.  I am not exactly sure of a great way to handle this, but here are 2 scenarios.

1) I was trying to evolve bipedal motion, but the thing keeps following over, then the one that can squirm the best is selected for.  I would like to be able to maybe pick a Joint in the creature and stipulate something along the lines of, if this joint drops below a certain vertical height then drastically decrease the fitness of the creature.  Hence creating a pressure to select for the creature to stay upright.  Also, there are creature that stand upright initially, but they get selected against because following over moves the creature further.

2) When my creature all start hitting 100% fitness, then evolution no longer selects for improvement.  For instance I can get 45.63 m/s on Generation 9 and then 12.7 m/s on Generation 57 for the Running Simulation because both produce a fitness of 100%.

Another thing I think may be cool would be to change the fitness equation.  For instance, train something to stand upright, then train it to walk, then train it to walk and jump.  Instead of having to start at square 1 for each task.