There was one problem I had with Skyrim that is fixed by a mod.
Throughout the game, you're told that WIndhelm is a racist city. It's the home of the Stormcloaks and has a strong idea of Nords before everyone else. You're told that the Dunmer have to live in a poor area of the city and Argonians aren't even allowed in the city. I play as an Argonian and when I entered Windhelm, a short scene happens just as in every city that begins a quest, but nothing else. I can go through the city as an Argonian without any problems, no one even noticing that I'm an Argonian. There's a mod called Inconsequential NPCs and among the other random NPCs added to the game, if you play as an Argonian a guard approaches you, telling you "Your kind aren't welcome in this city. You need to leave."
I agree that it this is a problem, but I don't really see a good way to fix this. There would be multiple options:
- Bar off Windhelm to an Argonian player. This would cut a lot off content from the Argonian player, make quests unwinnable and would be very confusing to players ("There needs to be a way in" - "There isn't, not at least not until a certain endgame quest")
- Make a specific Windhelm questline just for Argonian players. This would be good for Argonian players but bad for everyone else, because some of the limited resources are spent on content that only a fraction of the players will ever get to see
- Cut the lore, making it a worse story
This is a general problems for RPGs, especially those centered around a single character. Players want a lot of customization, but the developers don't have time to balance and design content for every single combination. So you either end up in the situation where a lot of the customization is mostly inconsequential - a stat boost here, a throwaway line there. Or you have a million of combinations, but only a few of them are actually good and viable on higher difficulties, which means that most of the customization options are just newbie traps and create an artificially inflated feeling of choice.