The advantage of the N64 approach is that it allows both the D-pad and analog stick to be primary inputs. They're both ideally positioned under the thumb, because they're the only input the thumb needs to interact with. It's a tradeoff between the number of available inputs and ergonomics. Every other controller has to compromise on one or the other. e.g. The DualShock is obviously a SNES controller with two sticks slapped in the middle, but since it was an update to the standard (D-pad focussed) PlayStation controller, they're not at the angle where your thumb naturally rests. Successive PlayStation controllers moved the stick up and out slightly to bring it more in line with the thumb.

The Saturn 3D Control Pad along with other "modern" controllers like the Xbox line, GameCube and Switch have the opposite layout, where the analog stick is the natural resting place for the thumb and you crane to reach the less-accessible D-pad. With the benefit of hindsight, this is probably the "right answer", because most games since the fifth generation are designed around the analog stick, with the D-pad occasionally used as four additional action buttons which you either don't need at all, or only use sparingly. I don't know that this style of game (e.g. tactical shooters with squad orders on the D-pad) really did or could have existed in the N64 generation, so the lack of D-pad access ends up being irrelevant to the kind of games that were actually coming out in the era.

If you released a console today with the N64 controller, that would be a terrible idea, because there are the kinds of games coming out that expect you to have four triggers, two analog sticks and reasonably convenient access to the D-pad. But I can't think of any N64 games that were worse because you couldn't access the D-pad. What games needed those extra inputs? What games didn't get made because those inputs weren't convenient? Coming at it the other way, what games were released for the Saturn 3D Control Pad that wouldn't have been possible on N64?