Part of it is low-ish expectations after TMP but also that with all the classic and TNG films that came later it still seems by far the boldest, having Kirk's mistakes from the past catch up with him, giving him a really great villain, making Kirk flawed but still pretty awesome, acknowledging that new, younger characters are coming in and having Khan's revenge almost succeed, the climax believably having to involve real sacrifice. Things like the eels also make it stand out as unusually intense and more successful for that.
Of the other films most feel pretty small, unsurprising, TUC and FC are the only other ones that felt really ambitious and both, especially their endings, still feel a little standard.