From PRD:
Alien Presence (Ex): A juvenile or older outer dragon has an aura that functions as frightful presence with a range equal to 30 feet × the dragon's age category. The effect of each dragon's alien presence is noted in its description.
So, the effect of each dragon's alien presence is unique to their type. That's why it is different from frightful presence, for although it's a fear effect, they have special effects exclusive for each dragon breed. This ability is what makes them so special and "alien" when compared to the other true dragons, and the unique effect is what makes it different from frightful presence.
Lets take a look at some of the alien presence effects of three different outer dragons:
Time dragon: A creature that fails its saving throw against a time dragon's alien presence is staggered for 5d6 rounds (or stunned if it has 4 Hit Dice or fewer).
Vortex dragon: A vortex dragon's alien presence bends space. A creature that fails its saving throw treats all other creatures as if they were under the effects of blur (or displacement if the target has 4 or fewer Hit Dice) for 5d6 rounds.
Lunar dragon: A lunar dragon's alien presence affects opponents that fail their saves as touch of idiocy (or as feeblemind for creatures with 4 or fewer Hit Dice) for 5d6 rounds. This is a mind-affecting compulsion effect.