He isn't. He accelerates slower and his top speed is also lower in the 3D games. There's a reason why you are doing a lot less platforming in the 3D games.
No, and I can prove it.
Mario's canon height is 155 cm. In Super Mario World, Mario is 20 pixels tall when short, and 28 pixels tall when tall. This implies that short Mario in Super Mario World is about 110.7 cm tall. This study shows that Mario's running speed is 9.1 Small Mario's per second, which translates to 10.0737 meters per second.
In Super Mario 64, Mario is 161 in-game units tall. His maximum running speed is 48 units per frame. Since there are 30 frames per second in SM64, that's a speed of 1440 units per second, or about 14.957 meters per second.
Love and tolerate.