Just encountering Pokemon will only add their name to the Pokedex - in Pokemon Black/White you have to catch the Pokemon in order for them to be added to the Pokedex in more than name only, which is why your battle encounters are not being added.
The Battle Subway Pokemon encounters won't be added to your Pokedex. The Battle Institute encounters also will not be seen.
If you have Wifi, sign up for the Pokemon Global Link service to gain access to the Dream World. By visiting the Dream World in Black/White, you will be able to befriend Pokemon you would otherwise have to transfer or trade to obtain.
It appears (from reading various forums) that you cannot just "see" Pokemon in the Global Battle, either, for them to add to your Pokedex - you have to "see" the Pokemon in the game itself (either from other trainers, trades, or in the wild) for them to add to the Pokedex.