I went to thea Chiikawa pop-up store of Chiikawa today.

I went to the pop-up store of Chiikawa today.

Chiikawa is a Japanese cartoon whichthat is very popular in Taiwan, so I had thought the line would behave been extremely long.

"That," instead of "which."
Correct use of the preterite and past perfect.

But tThe staff had asked me to scan a QR code and to return to the shop when I got a message, so I didn't have to line up in the hot weather.

"But" is not needed.

The way they manage the waitingorganize the queue is quite thoughtful.

HoweverBut, the items in the store weren't as numerous as I expected.

I only bought only a doll charm and two stickers.

I went to thea Chiikawa pop-up store of Chiikawa today.

Chiikawa is a Japanese cartoon which is very popular in Taiwan, so I hadoriginally thought the line would be extremely long.

I would use 'past perfect' only if there was a subsequent event in the same sentence. Saying 'originally' would deliver the same message, but it feels more intuitive as a listener.

But instead, the staff asked me to scan a QR code and return to the shop when I got aupon receiving their message, so I didn't have to line up in the hot weather.

It would be better to specify the 'message'.

The way they manage the waiting iqueue was quite thoughtful.

However, the items in the store weren't as numerous as I had expected.

如果有一家以上的 Chiikawa 商店，那就更好了： I went to thea pop-up store of Chiikawa store today.

Cf. https://en.wikipedia.org/wiki/Chiikawa

ButHowever, the staff asked me to scan a QR code and return to the shop when I got a message, so I didn't have to line up in the hot weather.

NOTE: When speaking, "But" is fine. When writing, the word "However" is better. (Writing in slightly more formal than speaking.)

In British English: The way they managed the waiting icue was quite thoughtful.¶
In American English: The way they managed the line was quite thoughtful.

I went to thea Chiikawa pop-up store of Chiikawa today.

Something closer to what you wrote but more natural: "I went to a/the pop-up store for Chiikawa today."

Chiikawa is a Japanese cartoon which is very popular in Taiwan, so I had thought the line would be extremely long.

The "had" is OK, but it's slightly more natural without it. Keep in mind that this sentence implies that the line was not long in reality -- like "I thought the line would be long (but it wasn't)."

If you wanted to just say more directly without the implication: "... so I figured the line would be extremely long."

But the staffHowever, an employee asked me to scan a QR code and return to the shop when I goet a message, so I diwouldn't have to line up in the hot weather.

Starting with "however" is a bit more natural here as a sentence beginning.

It's not completely necessary, but the subjunctive here sounds a little better to me rather than past tense.

The way they manage the waiting is quite thoughtfulsmart.

"thoughtful" usually means more like to consider the feelings of others in a very personal way. For example: "I can't believe he got me my book as a gift. It was so thoughtful!"

However, the items in the store weren't as numerous as I expected.

Yours is fine, but a bit less literary: "However, there weren't as many items in the store as I had expected."

I only bought a doll charm and two stickers.

This is fine, but I would personally connect this to the previous sentence to create a longer, more fluid thought:

"as I had expected, so I only bought a doll charm and two stickers."