I tried battle subway and the battle institute, and none of the new encounters came to my Pokedex.
When I capture a Pokemon, the Pokemon goes to my Pokedex with a small Pokeball on his left side. When I fight some Pokemon, he goes to my Pokedex WITHOUT the small Pokeball.
Like when I fought Shauntal from Elite Four and Froslass came to my Pokedex. but in Gen V Froslass is ONLY available by trade.
In the Global trade you can only search for Pokemon that you saw at least once. I want get more Pokemons in my Pokedex, so I will be able to trade more (eg.: Tornadus is a Pokemon BLACK ONLY, I never saw him, and I can't look for him in Global trade)