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They are three, not of a kind, who, in the wild, you cannot find.
Against the odds, ever set to rival, you must find your center for survival.
Your journey begins, you and one, but the quest is far from done.
Countless more may win your heart, but these three, there since the start,
They form you, as you form them, at least until you start again.

Don't use a device to learn their names, that's all show and little game.

To help, hinder, or enhance your cause, please see this additional clause:

They dwell in the shadow of the Golden Son’s rise, which so often causes the twinkle in the skies.

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Based partly on the fact that raisinghellyer's comment said the answer is "juvenile," I'm going to guess that the answer is

Bulbasaur, Squirtle, and Charmander

They are three, not of a kind, who, in the wild, you cannot find.

The three starters and their evolutions are not found in the wild at all

Against the odds, ever set to rival, you must find your center for survival.

Each of the types is super effective against one other and weak to the other, and your rival always takes the one super effective against yours. The center for survival is a reference to the PokeCenters that can be found in every town/city, where you can heal/revive your Pokemon for free.

Your journey begins, you and one, but the quest is far from done.

You take one started at the very beginning of the game, and continue the game with them.

Countless more may win your heart, but these three, there since the start,

Again, these are the starters. There are at least 148 others in the world, but you will always start with one of these three.

They form you, as you form them, at least until you start again.

Your team is often based around them, though the next time you play through you may pick a different starter.

Don't use a device to learn their names, that's all show and little game.

Pretty sure this is a reference to the Pokedex, though I'm not sure if I would consider that a little game.

Hint:

Possibly refers to HoHo (credit to Going Hamateur), but again, not that familiar to gens past first

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    $\begingroup$ Thanks @Bailey M, I forgot exactly how to hide the lines, so I deleted it until I could figure it out. $\endgroup$ – WilliamKnapp Jul 21 '15 at 18:46
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    $\begingroup$ Also not past first gen much but I think HoHo could be referred to as a golden sun or something... The universe gets a bit more elaborate after the first i believe. $\endgroup$ – Going hamateur Jul 21 '15 at 18:50
  • $\begingroup$ You got it! Nice job picking up on the juvenile drop. The only thing I'd want mentioned is the center for survival: Pokemon Centers. The device is the Pokedex, and it just seemed like it helped identify pokemon more in the show than the game (probably because we knew them by the time we found them in the game). As for the pseudohint, maybe it will help if I refer to it as the Golden Son... $\endgroup$ – raisinghellyer Jul 21 '15 at 19:01
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I am going to guess:

Proton, Neutron, Electron

They are three, not of a kind, who, in the wild, you cannot find.

Yup that is 3. Also in nature protons don't really exist by themselves, H+ is actually H3O+, electrons generally are attracted to ions, charge flows by passing electrons ion to ion through holes. Neutrons I am actually much less certain.

Against the odds, ever set to rival, you must find your center for survival.

electron and proton are opposites. But they form around a nucleus (center).

Your journey begins, you and one, but the quest is far from done.

Makes me think of hyrdrogen atom, one e- one h+. The far from done part makes me think of fusion in hindsight, and eventually the atom grows beyond just the hydrogen and electron

Countless more may win your heart, but these three, there since the start,

Probably about quarks and leptons and other small stuff, but protons neutrons and electrons have still been around from the start. Also when talking about subatomic particles the term countless is quite valid.

They form you, as you form them, at least until you start again.

They form you. Not sure on the you forming them part. But the start again part could refer to matter being recycled example from star into human. (fun fact all elements higher than iron on the periodic table are from stars exploding!)

Don't use a device to learn their names, that's all show and little game. To help, hinder, or enhance your cause, please see this additional clause: They dwell in the shadow of the Golden Sun’s rise, which so often causes the twinkle in the skies.

The sun is fueled by fusion of particles but it happens in the core so we cant see it.

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    $\begingroup$ @Goinghamateur I only wish I could have crafted this riddle with your answer in mind. Very well thought out and explained, a pristine answer, but it'll likely make the intended answer seem juvenile. Before I give any real hints, I'll just say to look at the first and third lines together. $\endgroup$ – raisinghellyer Jul 21 '15 at 18:00

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