The joke on Galilee started a long time ago back in the time of Solomon, 1 Kings 9:

10Now at the end of the twenty years during which Solomon built these two houses, the house of the LORD and the royal palace, 11King Solomon gave twenty towns in the land of Galilee to Hiram king of Tyre, who had supplied him with cedar and cypress logs and gold for his every desire. 12So Hiram went out from Tyre to inspect the towns that Solomon had given him, but he was not pleased with them.

13“What are these towns you have given me, my brother?” asked Hiram, and he called them the Land of Cabul, as they are called to this day.

Cabul sounds like the Hebrew for good-for-nothing.

The whole thing about Galilee and Nazareth seems to be some kind of divine irony/comedy. Let's see the context, John 1:

43 The next day Jesus decided to leave for Galilee. Finding Philip, he said to him, “Follow me.”

44 Philip, like Andrew and Peter, was from the town of Bethsaida. 45 Philip found Nathanael and told him, “We have found the one Moses wrote about in the Law, and about whom the prophets also wrote—Jesus of Nazareth, the son of Joseph.”

46 “Nazareth! Can anything good come from there?” Nathanael asked.

“Come and see,” said Philip.

Jesus was collecting a bunch of Galilean disciples, heading to Galilee.

John 12:

21 They came to Philip, who was from Bethsaida in Galilee, with a request. “Sir,” they said, “we would like to see Jesus.”

Nathanael himself was from Galilee, John 21:

2 Simon Peter, Thomas (also known as Didymus), Nathanael from Cana in Galilee, the sons of Zebedee, and two other disciples were together.

Ironically, where was Nazareth?

Barnes:

Nazareth - This was a small town, situated in Galilee, west of Capernaum, and not far from Cana.

At the time of Nathaniel, Jews had a prejudice against Galilee which included Nazareth.

John 7:

41 Others said, “He is the Messiah.” Still others asked, “How can the Messiah come from Galilee?

John 7:

52 They replied, “Are you from Galilee, too? Look into it, and you will find that a prophet does not come out of Galilee.”

What was worse than Galilee?

Nazareth :) Smiley face intended.

Gill:

The whole country of Galilee was had in contempt with the Jews; but Nazareth was so mean a place, that it seems it was even despised by its neighbours, by the Galilaeans themselves; for Nathanael was a Galilean

Nathanael was a Galilean. Nazareth was part of Galilee. Jesus was taking his disciples back home to Galilee.

John 1:

46“Nazareth! Can anything good come from there?” Nathanael asked.

Why did Nathaniel say, "Can any good thing come out of Nazareth?"?

He was just innocently echoing the prejudice of the day.

“Come and see,” said Philip.

In some sense, Philip prophesied to Nathaniel to go with Jesus and he would clear his prejudice.

47 When Jesus saw Nathanael approaching, he said of him, “Here truly is an Israelite in whom there is no deceit.”

Jesus confirmed Nathanael's innocence and sincerity.

The whole thing about Galilee and Nazareth seems to be some kind of divine irony/comedy. Nazareth was the butt of the joke. Let's see the context, John 1:

43 The next day Jesus decided to leave for Galilee. Finding Philip, he said to him, “Follow me.”

44 Philip, like Andrew and Peter, was from the town of Bethsaida. 45 Philip found Nathanael and told him, “We have found the one Moses wrote about in the Law, and about whom the prophets also wrote—Jesus of Nazareth, the son of Joseph.”

46 “Nazareth! Can anything good come from there?” Nathanael asked.

“Come and see,” said Philip.

Jesus was collecting a bunch of Galilean disciples, heading to Galilee.

John 12:

21 They came to Philip, who was from Bethsaida in Galilee, with a request. “Sir,” they said, “we would like to see Jesus.”

Nathanael himself was from Galilee, John 21:

2 Simon Peter, Thomas (also known as Didymus), Nathanael from Cana in Galilee, the sons of Zebedee, and two other disciples were together.

Ironically, where was Nazareth?

Barnes:

Nazareth - This was a small town, situated in Galilee, west of Capernaum, and not far from Cana.

At the time of Nathaniel, Jews had a prejudice against Galilee which included Nazareth.

John 7:

41 Others said, “He is the Messiah.” Still others asked, “How can the Messiah come from Galilee?

John 7:

52 They replied, “Are you from Galilee, too? Look into it, and you will find that a prophet does not come out of Galilee.”

What was worse than Galilee?

Nazareth :) Smiley face intended.

Gill:

The whole country of Galilee was had in contempt with the Jews; but Nazareth was so mean a place, that it seems it was even despised by its neighbours, by the Galilaeans themselves; for Nathanael was a Galilean

Nathanael was a Galilean. Nazareth was part of Galilee. Jesus was taking his disciples back home to Galilee.

John 1:

46“Nazareth! Can anything good come from there?” Nathanael asked.

Why did Nathaniel say, "Can any good thing come out of Nazareth?"?

He was just innocently echoing the prejudice of the day.

“Come and see,” said Philip.

In some sense, Philip prophesied to Nathaniel to go with Jesus and he would clear his prejudice.

47 When Jesus saw Nathanael approaching, he said of him, “Here truly is an Israelite in whom there is no deceit.”

Jesus confirmed Nathanael's innocence and sincerity.