Curate, connect, and discover
I know it's a meme that Shindou cries a lot, and I'm totally guilty of snorting at it, but to be completely fair, I don't exactly recall him ever crying without a very good reason to. Most of the time he's crying from frustration and helplessness, which is very understandable, especially given he's, like, 14. The adults all around him are failing him, all the while he has enormous responsibility put onto his shoulders. He's forced to comply with Fifth Sector's orders or risk not only literally getting beaten up, but also risk getting everybody else beaten up through sheer association with him.
Aside from that, instances of him crying in other seasons that I recall are:
Crying while thinking about the kind girl that helped him that he would never see again, because they're literally from different time periods.
Crying after the first match of Shinsei Inazuma Japan after being utterly humiliated in front of the entire country, and having no idea why any of this was happening.