Question

What do I do after I defeat all 16 gyms & the elite 4 two times?

Answer 1

If I'm not mistaken, you have not much left to do with the story.
All you have left to do are:
1. fill your Pokedex. (you will need to trade from other games like SS)
2. go shiny hunting.(for your usage or trading)
3. train the pokemons to Lv.100 with EVs and such so that they can be awesomely strong to battle other people's.decide your teams 1st though.there isn't any point in training individually because you need to decide the moveset or role of a pokemon.
4. wait for the events and go get those event presents. Because, some event things can unlock secret places, catch secret pokemons for your story.

Edit: Credit to Victini Victory. These are his answers. Wanting to add some links for someone who just started playing to be able to know, I added here.+his comment.

• You can go to Mt.Silver and defeat Red on the top.
• You can then get a Kanto starter from Prof. Oak.
• And a Hoenn starter from Steven Stone at Silph Co., Saffron City.
• Catch Kyogre after obtaining the Blue Orb from Mr.Pokemon, at the Embedded Tower
• Catch Mewtwo in Cerulean Cave.
• Catch Latias in Kanto.
• Catch Entei, Raikou, and Suicune.
• Get someone to give you a Groudon from Soulsilver, that way you can catch Rayquaza at the Embedded Tower, after getting the Jade Orb from Prof. Oak.
• Level your Pokemon up to Level 100.
• There's the obvious Pokedex to fill up.
• And lastly, catch Lugia at Whirl Islands.

Comments

I put another answer, you can edit that stuff in if you want.

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And I'll hide mines.

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sorry,which one are you? oh btw,leave above comments like that. that's ok.

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I am a boy.