Number 1 - when pressing the retrain button please ask the player if they are sure they want to retrain the character in case pressing the button was a mistake. My wife just accidentally pressed retrain while trying to apply her skill point for reaching 32nd level. I've always been afraid of doing that myself so I restrict myself to the double-click commit. The placement of and triggers for those two buttons seem like terrible GUI design.
An even better change - bring back the old retrain method that brings up a separate window that lets the player assign or unassign skill points (similar to how the Skill Planner website works) until they are done and then either cancel, changing nothing on the character, or commit the new skill tree to the character and spending the token at that time.
As long as retrain tokens cost Zen, the retrain process should be as smooth and reversible as possible or at least confirmed that a retrain is desired.
Is the number of retrain tokens available displayed somewhere? I haven't noticed.