Thanks for the feedback! We're still improving the controller support, so look out for improvements in that over development. The latest patch did some tweaks to the controller aiming so it should be a bit easier to use. Eventually we'll get around to adding controller re-binding as well.
The map has been fixed as well so it should update from the beginning of the level always now.
Also there is no persistence with mutations yet, but that should be added in the next week or two!