Minor issue I noticed, but definitely something that needs to be addressed:
Tool Proficiency granting the exact same bonus as a Skill Proficiency.
Specifically... I'm looking at the Disguise Kit. Several Backgrounds (like the Charlatan and Guild Thief) grant you proficiency in both Deception and the Disguise Kit. However... what does having a Disguise Kit get you? It allows you to add your proficiency bonus to your Charisma (Deception) check. Something you already get because you already have the Deception skill. If you have the Deception Skill... the Disguise Kit Tool is worthless. Basically those two Backgrounds are now one Tool short, because they are giving you proficiency in a Tool you don't need to use.
I can understand why you would want both the Disguise Kit Tool and the Deception Skill in the game... because certain Classes or Backgrounds might grant the Disguise Kit Tool without the Skill. Therefore allowing that person to gain the proficiency bonus to the specific check of rolling Charisma (Deception) when using a disguise and not on any other Charisma (Deception) check. But if you are granting a Class or Background the Charisma (Deception) Skill... there is absolutely no reason to also give them the Disguise Kit Tool, because it serves them no purpose. They need to replace that Tool with a different Tool or an additional language.
This exact phenomenon also applies to the Wanderer Background and his gaining both the Strength (Athletics) Skill and the Climber's Kit Tool. When you already have Athletics, the need for the Climber's Kit is made nil (because it grants proficiency in Strength (Athletics) checks to climb, which you already have with the Skill.)