I've also questioned the use of Tools as they stand, and I know the way I'm going to handle it (assuming it doesn't get changed down the line) is that Skills grant the proficiency bonus and Tools give you Advantage.
Here's my thinking: If you are trained in a particular skill, you can make more difficult attempts. Adding your proficiency bonus means that you can reach higher DCs than another character could. If you have tools, you have a better chance at doing what you already know how to do (thus gaining Advantage.)
If you are trying to pretend to be someone else... you only have so much ability to look different, sound different, move different, and act different. Use a Disguise Kit, you have a better shot at at least getting part of that (how you look) taken care of. But you still can't attempt higher difficulty masquerades because you aren't good at all the other stuff that go into it. It's only if you are Trained in Bluff that you have the ability to reach those higher DCs because you have more control over your voice, how you move and so on.
Now I know some people wouldn't like this rule because they'll trot out the "If you grant Advantage for using Tools all the time, then you can never grant Advantage as a situational bonus in the middle of the adventure." But for my money... using a disguise kit or a climber's kit or other tool *is* a situational bonus. How often are you as a DM really going to grant Advantage otherwise? There are plenty of reasons why you'd assign Disadvantage during a STR (Athletics/Climb) check... rain, heavy winds, etc... but what situations are you going to find to assign Advantage that aren't using rope, harnesses, or belaying devices? Having a climber's kit available is the most obvious and likely situational bonus you're ever going to find.
To me... Skills and Tools need to both grant bonuses. And since I don't like the idea of stacking proficiency or stacking Advantage... having each one grant one of the bonuses is the best way I think to go.