To be fair, I believe balance is something you do for a mechanic, and a mechanic is something you implement into a game. Balance, to be fair however, can be a pain sometimes. Especially with a large cast/enemies/mechanics.
That said, I believe the hardest thing to implement into a game is any form of diverse lighting. Now, keep in mind, this is coming from someone that very much still needs to learn a lot (an amateur), but when I have to adjust lighting or if some character has to hold a lamp or flashlight, I have a hard time.
Additionally, any time I have to do some eventing, and there's a lot of variables involved that changes up said cutscenes. It's still something I have trouble with.
I'm still having a hard time implementing a CCG type function >_< I almost had it in VXA, but then my puter gave up the ghost and took the backups with it. (lesson learned: keep a hard copy of your code!) I hadn't used JS in a decade so I'm rusty AF and banging my head on my desk trying to get it working in MV.