The sheer length of the game. You go through an entire school year, which isn't uncommon, but it becomes lengthy because you're required to plan Hitomi's daily actions at three day intervals. The only skippable parts are the Visual Novel events- making it much more time-consuming than typical otome games (where players are only required to make choices and the rest of the game is largely skippable).
The "decision point" in the character routes, which is best described as a fork in the road where one sign ("choice") directs you to the "friendship ending", and the other, the "lovers ending". Of course, the game never specifies which set of choices does this, so it's entirely possible to play a chunk of the game with no idea as to if you're heading down your desired ending.
To make it worse, some characters have choices not a part of the "decision point" that when made, makes it impossible to achieve the "lovers" ending for the rest of that playthrough. The only way to get around this is if you're lucky enough to have saved before making those choices... or you're starting again from day one. Oh, and to put the cherry on top of the sadistic cake, some characters have multiple "instant no-lovers ending" sets of choices.
Some events can only be triggered by having a certain level of affection, being a certain weight, having a certain stat amount, etc. Same goes for certain items and C Gs.
To ask a character out on a date, whether they accept or not is based on probability. Thankfully, the likelihood of being rejected decreases as the guy grows to like you... but this can be frustrating for some in the beginning, especially with Ren.
Tear Jerker: Ayato's route, especially his friendship ending, where it is heavily implied that he succumbed to his illness.
Also in Ayato's route, when he is hospitalised, he becomes friends with a boy about the same age as him in the room next door named Yoshihisa. Yoshihisa also suffers from the same illness as Ayato. When pursuing Ayato's love ending, Yoshihisa dies the day after the Christmas party.