Alienation and isolation play a part in both "The Wild Swans at Coole" and "Araby."
Though the swans possess what the speaker lacks--they are "Unwearied still, lover by lover," and "Their hearts have not grown old;/Passion or conquest, wander where they will,/Attend upon them still"--the speaker is able to count only 59--not sixty. One swan is left out.
And the speaker is alienated and isolated and contrasted with the swans--again, at least 58 have what he doesn't.
The speaker sees the swans as immortal--of air and water--while he is mortal--of land. The nineteen years that have passed since he first saw the swans haven't changed them, as the years have changed him.
In "Araby," the speaker at first feels a part of his world. He plays with his friends, feels grounded in his church, and sees himself as having a relationship or at least a strong possibility of one with Mangan's sister. Yet, these prove largely to be illusion.
During his epiphany at the bazaar (Araby), he realizes that he is not a spiritual hero on a quest to woo a Virgin Mary-like lady (Mangan's sister), that the bazaar is just a trivial way for his church to make money, that he really means nothing to Mangan's sister anyway, and that he has been trivial and silly himself.
Thus, "Araby" closes with the narrator feeling isolated and alienated from his church and his object of affection. Though his epiphany is an awakening of sorts--he begins the story figuratively blind and is freed from his blindness by the epiphany--his realizations do result in isolating him.
At least, in contrast to the speaker in "Wild Swans," the adolescent narrator of "Araby" still has his friends, as far as the reader knows.