That's actually not true at all. You still had to choose a star before you start a level just like in all other 3D Marios after it. Banjo Kazooie had more freedom than any Mario game.
Yes, but you still had more freedom in M64 than any other even if you choose a star in the beginning. In most cases you basically had the same stage structure/design no matter what you choose, enabling you to get any star, whereas after M64 it got too specific. This is actually good, AND bad.