Reselecting tools after each craft should be removed. Once you select your tools, they should be remembered for the next craft until you select a new recipe or close out of the crafting window. Also, when the craft window shows 0/1 of the materials that you need to craft, the 0 should be able to exceed past 1. So lets say you place 20 materials inside of the craft, it would say 20/1.
In addition, there should be another button. One button saying "craft", the other saying "craft all". Clicking on "craft" will only craft one item. Clicking on "craft all" will craft all the items, one after the other. This is used by many crafting systems and it should be the same with Xsyon. This will dramatically reduce the amount of clicks as well.