I used to use up on control stick for 5 years of Melee play before I made a conscious decision to change x/y in an attempt to gain more jumping control (I played - and still play - Ganondorf and badly needed that jump control). After I switched, I never effed with the control stick until I started realizing that certain situations call for it. That is to say, certain scenarios are far more difficult or simply impossible if tap jump is off.
These examples will be for Ganondorf, but you can at least get the idea of why tap is effective here. First, say your opponent is above you on BF. If I want to uair that guy who is just chillin on a platform, it's easier to hop (or SH) up with the control stick, leave the stick up and tap the A button to execute the uair than it is to tap the x/y button and the either up+a or c-stick up. This is because your thumb doesn't have to move at all in the tap scenario while with the x/y scenario, you have to slide your thumb from x/y to A. It may only be a matter of a frame or two of difference, but that may land the hit before the shield comes out.
Also, I find that while most of the time I thunderstorm (chaining lagless SH dairs) with the control stick + down c-stick, sometimes I hold down on the control stick and slide from x/y to A. It all depends on the situation, and specifically, I think it depends on the positioning of my hands on the controller at any given moment. There's always a case in which one method is more effective/efficient than the other.
Ultimately, I think of the tap jump debate like I think of the other moves in smash that have multiple inputs. Just like Z vs R+A (grabs) and c-stick vs direction+A (smash attacks), I think it's important to use and feel comfortable with both jump inputs. There's always one input that is a better choice than the other and it's just a matter of figuring out what input that is for every possible situation.
