Annivia is one of the original champion in league, and as you can see from Azir and Gnar, the greener a champion the more complex his/her/its kit is.
However, she is still above average in terms of difficulty. Although Q is a long ranged pass through skill shot, it is also extremely slow and requires precise timing to land both the impact and detonation damage.
As well, before 6, she has some mana problems and can't do damage without chilling the enemy first. Essentially, this means that her early game is extremely dependent on landing the slowest skill shot in the game.
However, after 6 her difficulty drops off significantly. Ult and E combo is as easy as any point and click, and the enemies will be slowed to make Q fairly easy to land. After accumulating enough mana and mana regen from items and levels, mana management becomes a non-issue.
Compared to other champions with equal difficult ratings (ie. Rumble, who has all skill shots and can CC himself. Or Yasuo, who has one of the lowest HP and MR in game AND is a melee with a conditional ult) she does seem to be a bit easy,
But ultimately, she was difficult, and was probably the most difficult champion relative to the others at release.