In this case, I have been trying to convert a video game (Dragon Quest VII) into a 3.6 D&D adventure. I love the concepts behind the game: discovery, time-travel, mysteries, class-building, and of course good vs. evil. There are some elements that I don't care for: some fetch questing and some just bizarre story and gameplay ideas that I have needed to change or remove entirely. On the whole, however, the game has been running fine.
My biggest problem is that video games can force their players into situations that role-players would avoid or would resent having forced upon them. Usually, I have several contingencies for the possibilities that I can envision, but sometimes players are just stubborn (or get a perverse pleasure about messing with the DM). The key (and I sometimes forget this) is to remember that the point of the game is to have fun, not to get over-burdened with rules and plot-lines.
Due to a change in circumstances in the last game in this campaign, I have had to rework the situations that my players are going to have to face. Currently, their abilities have been robbed from them, but their equipment remains (I wasn't sure if they were going to play in a way that let them keep their equipment or not). Thus, the situations can't be quite as dangerous as their character levels would usually suggest, but they can't be so weak that the players don't get a sense of accomplishment from their adventure. It's a difficult balance to maintain, especially in a game where the luck of the die can change everything.
My lessons and writings often don't go as planned either. Usually, I can predict how my students or my stories are going to react to certain conditions, but that is not always the case. Still, I think that most things work out well in the end.