Well an Ocarina is an instrument, so I don't think gears would work. Unless they were musical gears :O And I wanted Gallade to be Adult Link very badly. Maybe I could make him somehow turn into a Gallade as a result of his soul being in the Light Temple for 7 years. I'll have to think about it.
Or, alternatively, just stick with keeping the Young Link = Ralts idea. It avoids making the idea crackier and more convoluted than it really should be (because then you'd have to explain why he turned into a Gallade specifically) while at the same time avoiding creating a pairing of two Pokémon that can't actually breed. (No member of the Ralts line can breed with any member of the Seedot line, so Nuzleaf x Kirlia wouldn't actually work. Meaning, yeah, no childhood crush or anything like that.)
By the way I'm making Link a silent protagonist because I want to stay true to the originals.
While this is an interesting idea, it also means your work is probably going to be extremely difficult because a lot of characterization will ride on what your character says. Silent characters sometimes have the tendency of sounding flat because it looks to a reader as if all they're doing is going through the motions of the story like they're puppets, without any real reaction to what's going on. (Especially if you're restricting internal dialogue as well.) It's really something you do only when you're experienced with writing enough to pull it off, so my advice would be to create some dialogue anyway. (Remember that there's been comics and cartoons that have Link speaking, and in the games, it's likely that he says something we just don't really "hear" in order to interact with various NPCs, if that makes sense.)
As for the story, I haven't really played any of those games to be honest, so I can't really comment on whether or not it's a good or bad idea. I can say that it might be a good idea to avoid making this just a carbon copy of the games with Pokémon inserted in. It's okay to deviate a little and keep in mind that Pokémon have their own powers and their own set of myths themselves. Remember to blend that in so it's not just Ocarina of Time with Pokémon but instead a crossover between the two.
Also, it might be better to just focus on planning for one story at the moment instead of setting your sights for three. That way, you can work hard at building up and refining the details of one particular story, so all your time and effort isn't divided (which would probably weaken your first story). That and if it turns out to be something you don't want to do, you won't lose tomes of work.
Not sure if this all makes sense. A bit distracted right now. If it's not, feel free to ask.