If you're making a game that breaks from convention, set that expectation early and show the player — force them to understand — through level design how yours differs, but also note that some players won't want to cooperate and will need to be subtly prodded back on track.
Super Metroid got included? No surprises here. But apart from it establishing its differences early on compared to other platform games, Super Metroid is also subtle in teaching you new skills further down the road.
The animals on Zebes are an overlooked topic as they teach by example: both the Dachora and the Etecoons perform actions in the background of the game's environment which you can attempt to copy. In the case of the Dachora it teaches you how to shinespark:
In the case of the Etecoons you are taught an even better trick: walljumping.
The funny bit is that these work regardless of meeting these critters, these skills are simply innate to the player and cannot be unlearned (unlike Assassin's Creed's hard-coded "skills"). As most of the game is designed around normal movement, knowing these skills beforehand gives you an advantage. Your first experience of Super Metroid is substantially different than a second play-through, and it even influences how you play other instalments.
That might go a bit further than just a tutorial: it imprints a certain move set, so that after distancing itself from conventional platform games during the tutorial, it creates a separate genre definition all for itself in your brain, which works as a kind of internal branding.
This is also why I never regarded Metroid Prime as a proper sequel to Super Metroid, despite it being a superb game in itself. It simply missed the response to the imprint's call, while both Metroid Fusion and Metroid: Zero Mission, picked up that particular ball and ran with it.