I simply wish more games put more effort into integrating story and gameplay together. Oftentimes, all you really have to do is pat the player on the head and gently let him down, when he succeeds at something unexpected or does something he really shouldn't. I don't even know if devs can't implement that due to difficulties, or don't realize how many details they are missing. There must be some testers that will note every stupid permutation of variables that writers will have to consider.
Why can't stories and mechanics be friends? Stories are often viewed as systems, not inviolable ones, but still subject to certain rules. Mechanics are how player interfaces with the game, and thus can elicit visceral emotional responses. I genuinely don't think any game portrayed the one-man-army aspect of player characters better than Westerado Double Barreled. And it's shown in a very simple way. I genuinely don't think there is any magic system more interesting than one in inkle's Sorcery. And it's just about putting in effort to write out all the consequences for different spells.