It sounds like you'll be wanting to play with the Original Spells module then. I made that version precisely because of that kind of feedback. The Enhanced Spells version is honestly just there as a legacy, really. It might be better to call it the "New Spells" module, since both versions have improvements to the combat arts. The whole point in the continued existence of Enhanced Spells is that it replaces old spells with new ones. So I'm not going to start switching them back. Players who want their favorite old combat arts should use Original Spells instead.
You can, it's in creatures.txt. These are all the Inquisitor skills:
mgr.addCreatureSkill( 51, {skill_id = 1, advanced = 1, skill_name = "skill_sword_lore", })
mgr.addCreatureSkill( 51, {skill_id = 2, advanced = 0, skill_name = "skill_hafted_weapon_lore", })
mgr.addCreatureSkill( 51, {skill_id = 3, advanced = 0, skill_name = "skill_armor_lore", })
mgr.addCreatureSkill( 51, {skill_id = 4, advanced = 1, skill_name = "skill_distance_weapon_lore", })
mgr.addCreatureSkill( 51, {skill_id = 5, advanced = 1, skill_name = "skill_pole_arm_lore", })
mgr.addCreatureSkill( 51, {skill_id = 6, advanced = 0, skill_name = "skill_offhand_weapon_lore", })
mgr.addCreatureSkill( 51, {skill_id = 8, advanced = 0, skill_name = "skill_wizzardstaff_lore", })
mgr.addCreatureSkill( 51, {skill_id = 9, advanced = 0, skill_name = "skill_tactics_lore", })
mgr.addCreatureSkill( 51, {skill_id = 10, advanced = 1, skill_name = "skill_speed_lore", })
mgr.addCreatureSkill( 51, {skill_id = 11, advanced = 0, skill_name = "skill_damage_lore", })
mgr.addCreatureSkill( 51, {skill_id = 12, advanced = 1, skill_name = "skill_shield_lore", })
mgr.addCreatureSkill( 51, {skill_id = 13, advanced = 1, skill_name = "skill_constitution", })
mgr.addCreatureSkill( 51, {skill_id = 14, advanced = 0, skill_name = "skill_toughness", })
mgr.addCreatureSkill( 51, {skill_id = 15, advanced = 0, skill_name = "skill_combat_reflexes", })
mgr.addCreatureSkill( 51, {skill_id = 17, advanced = 0, skill_name = "skill_combat_disciple", })
mgr.addCreatureSkill( 51, {skill_id = 18, advanced = 1, skill_name = "skill_concentration", })
mgr.addCreatureSkill( 51, {skill_id = 19, advanced = 1, skill_name = "skill_ancient_magic_lore", })
mgr.addCreatureSkill( 51, {skill_id = 20, advanced = 0, skill_name = "skill_horseman", })
mgr.addCreatureSkill( 51, {skill_id = 21, advanced = 1, skill_name = "skill_armorer_apprentice", })
mgr.addCreatureSkill( 51, {skill_id = 23, advanced = 1, skill_name = "skill_spellresist_lore", })
mgr.addCreatureSkill( 51, {skill_id = 24, advanced = 1, skill_name = "skill_alchemist", })
mgr.addCreatureSkill( 51, {skill_id = 25, advanced = 0, skill_name = "skill_trader", })
mgr.addCreatureSkill( 51, {skill_id = 27, advanced = 1, skill_name = "skill_perception", })
mgr.addCreatureSkill( 51, {skill_id = 29, advanced = 0, skill_name = "skill_devotion", })
mgr.addCreatureSkill( 51, {skill_id = 36, advanced = 0, skill_name = "skill_IN_inquisition_focus", })
mgr.addCreatureSkill( 51, {skill_id = 37, advanced = 1, skill_name = "skill_IN_power_focus", })
mgr.addCreatureSkill( 51, {skill_id = 38, advanced = 1, skill_name = "skill_IN_underworld_focus", })
mgr.addCreatureSkill( 51, {skill_id = 51, advanced = 0, skill_name = "skill_IN_power_lore", })
mgr.addCreatureSkill( 51, {skill_id = 52, advanced = 0, skill_name = "skill_IN_underworld_lore", })
If it says advanced = 0, it's a left column skill, if it's advanced = 1, it's in the right column. You can change them as you see fit. I don't plan on making any such changes in Enhanced Edition.