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That looks pretty cool! When did you reach a plateau for the creature? If you aren't done with your creature yet and wanted to possibly reach more realistic motions, you would need to change the neural network. Using the neuron calculator by Zelk12, for 3 layers like you have now you would need 35 neurons rather than 10, because you have 61 muscles/outputs. If you added a layer you could do the first layer as 20 neurons, and then the last layer at 35. 5 layers would take a very, very long time, but the layers would go like 11,20,35.

This one reaches a plateau around 28% - 40% fitness. I will try for sure your suggestion of neural network.

When using the calculator, what determines the amount of inputs?

As far as I know, there will always be 11 inputs. Probably things such as speed, time, position, but I'm not sure.