Defeating the last gym leader will allow all Pokemon to obey you regardless of level.
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It's due to to high a level and not enough badges. The more badges you have, the higher level pokemon will obey. A level 100 will not obey until all of the gyms have been beaten.
These are the Gym Badges that make your Pokemon obey:Knuckle Badge: Pokemon up to level 30 obey you.Heat Badge: Pokemon up to level 50 obey you.Feather Badge: Pokemon up to level 70 obey you.Rain Badge: All Pokemon regardless of their level will obey you.
Badges allow Pokemon obey to a certain level. Once you get all badges, any traded Pokemon will obey at any level.
Once you beat a gym leader you can get a certain level of pokemon to obey you.
in Pokemon pearl / diamond you need 2 badges for any Pokemon up to level 20 to obey you need 4 badges for any Pokemon up to level 40 to obey you need 6 badges for any Pokemon up to level 60 to obey you need all 8 for any Pokemon (even traded) to obey in heart gold / soul silver its exsacly the same :)