Rayquaza and deoxys are the best ...
or at least for me....
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USE A FIAH TYPE.
The Gym Leader Clay Uses Ground Types.
The Hearthome gym leader Fantina lets you use surf in Pokemon Diamond, Pearl and Platinum.
no you can't
The fifth gym leader Koga uses Poison type pokemon so your best bet is to use Psychic or Ground types against them. A Kadabra(Alakazam would be even better) can easily take care of all of Koga's pokemon.