You could alter your Scene_Menu to include an option for the skill-tree, or better yet, alter Scene_Skill. For example, in the update method of Scene_Skill,
if Input.trigger?(Input::X)
$scene = Scene_SkillTree.new(@actor_index)
end
should work, if you're having trouble doing this just ask me to do a rewrite of the class for you.
LE EDIT:: Alternatively, stick this below the skill tree script, but still above main.
class Scene_Skill < Scene_Base
alias pac_deity_skltr_updsklselect update_skill_selection
def update_skill_selection
pac_deity_skltr_updsklselect
if Input.trigger(Input::X)
$scene = Scene_SkillTree.new(@actor_index)
end
end
end