Pokemon Trainer: Link

I feel like he needs a Beedrill to represent The Good Bee from Link to the Pask and a Rowlet for Kaepora Gaebora from OoT and MM. Past that, very good choices representing Epona with a Rapidash, Midna with a Sableye, and the Master Sword/Fi with a Honedge (I can see Fi needing/using a special "Reflect Stone" or learning the Reflect move in order to evolve into a Aegislash instead of evolving normally).

I'll admit I didn't recognize the final pokemon and had to look it up (it's a Cottenee), but understood it represented Navi, which is a very good choice in terms of typing, as I would have chosen a Flabebe or Floette based on appearance. Celebi for Navi would have also made a good choice for Navi considering her origins in OoT and the theory that Navi is the Great Fairy in Twilight Princess.

The Navi Theory, for those who don't know, goes that Navi leaves Hyrule after OoT because she feels weak, unable to really help Link during his adventure, in order to learn from other Great Fairies, who teacher her elemental magic, not just healing magic. When Link does find her and they return to Hyrule, Ganondorf tries to take over, killing all the Great Fairies in Hyrule, who only know healing magic, but can't kill Navi because she's too powerful. Ganondorf gets defeated, leading to his banishment in Twilight Princess, while Navi creates the Cave of Ordeals, which serves two purposes. First, to draw in and imprison the monsters Ganondorf created with his dark magic, to help Hyrule rebuild. And second, to serve as Great Fountain and home for Hyrule's remaining fairies, where she teaches them healing magic, to further help the people of Hyrule, and elemental magic, which gets used on the monsters. Fairies that are especially powerful in certain types of elemental magic get chosen to become spirits inhabiting objects to help Hyrule's future heroes, such as the wind fairy in the Gale Boomerange in TP.