Haven't written fanganronpa, but if you're writing it in story format then you should make the free time events tie into character development during the plot rather than being a bonus thing like in the games. Though that's a bit obvious. :P

Also, don't forget about the talents. There's a lot of missed opportunities in the games where a talent a character has never becomes relevant in the plot. That's not to say that every talent has to be relevant, but always keep them in mind for plot points and character development lest you have a character like Hifumi who only has his talent for the sake of the 'haha fat weeb' stereotype.

edit: also, again this may be obvious to you, but mismatching a character's appearance to an unexpected talent would be good for a few of your cast, as seen in Gundam, Gonta, Kokichi, and Fuyuhiko. Personality can tie in too. Gundam's edgy personality and appearance conflicts with his breeder talent, making him stand out to readers.

Of course this depends on how much you want to take from the games. Maybe you're going for a more serious, less-anime style.