The ending of Step Up 3D settles three things at once: the Pirates win World Jam over Julien's Samurai crew, Luke and Natalie reunite at a train station, and Luke hands his sneakers to Moose, which makes Moose the new leader. In my opinion, that last gesture is the real ending, and the kiss is the warm bow on top.
It could be argued that the sneakers are the film's neatest piece of design. Moose finds Luke in the first place because he spots a stranger wearing rare sneakers, so passing them on closes a loop that began before Luke had a name. The shoes are a title belt, and Luke is not just leaving a crew, he is naming his successor.
Natalie's choice is the other half. After the betrayal over her brother, she does not win Luke back with an apology. She secretly arranges a film school place for him in California and invites him along. Perhaps that is why the reunion works: she offers him a future outside the warehouse, which is the thing he did not have when the building was lost.
Moose and Camille's kiss completes his own thread. He arrived promising his father he would stop dancing, and he leaves as the person who holds the crew together, with Camille beside him. That handoff pays off in Step Up All In, where Moose helps Sean build a new crew. Compared with Step Up 2 The Streets, where one dancer's two worlds collide, this ending is more about inheritance than choosing sides.