A good game that has a complex combat system, allowing for run and gun/stealth/whatever is one where all these options are viable. There is no dominant strategy because the game is perfectly balanced around all these different playstyles allowing for a player to mix and match, try new things. But a bad game with complex combat systems will have an obvious weak play style. The big part in all this is PUNISHMENT. See when a players preferred style of play for that game is weaker they feel like they are being punished for using it. Yes they enjoy playing it as stealth but it would be 10x easier to just use a rocket launcher to blast through them all. They sit there and say, "Why is the way I want to play weaker? You gave me this playstyle, but you made it bad. Why am I being punished for playing the way I want to play?"
In essence it feels like a punishment, like the game is saying, "No you shouldn't play like that, it isn't as good". Of course that only works for the play style bit of your OP.
As for the spell system and overpowered things in games, it comes down to two different things, challenge and choice. See if something like custom spells are overpowered then it removes challenge from the game, it messes with the all important difficulty curve which breaks a games flow. Once we've found something overpowered then it's a dominant strategy. When we have a dominant strategy then we venture into the idea that the game is less of a game and more of a puzzle. We have a solution that will always work. If we don't take the dominant strategy then we get back into the idea that it feels like we are being punished for not taking it. And this inhibits are choice. We may want to take the overpowered option, not because it makes things easier, but because it's how we want to play. But in doing so this destroys challenge, destroys flow, and forces us to feel like we have to choose the other path. So now we feel punished for taking the weaker option. It's this cycle of punishment or lack of challenge that can destroy enjoyment of a game.
The arguments for why you shouldn't be able to join every single guild in something like Skyrim is because of immersion I believe. It feels strange when every group in the game says, "Yeah you can join our club!" When in reality some of these clubs don't get along. Another aspect of it is the feeling of inclusion/exclusion. If you join Guild "A" and you can't join Guild "B" then you are part of something that others can't be a part of. Your character has something that other characters can't have. Of course I've always found exclusive Guilds, Factions, Skill Trees, etc. to be rather annoying. It just limits you, limits your story, limits a lot of things. Sometimes it might not make sense in a world but I'd rather have more options then be barred from something just because I made the "wrong" choice.
In essence it feels like a punishment, like the game is saying, "No you shouldn't play like that, it isn't as good". Of course that only works for the play style bit of your OP.
As for the spell system and overpowered things in games, it comes down to two different things, challenge and choice. See if something like custom spells are overpowered then it removes challenge from the game, it messes with the all important difficulty curve which breaks a games flow. Once we've found something overpowered then it's a dominant strategy. When we have a dominant strategy then we venture into the idea that the game is less of a game and more of a puzzle. We have a solution that will always work. If we don't take the dominant strategy then we get back into the idea that it feels like we are being punished for not taking it. And this inhibits are choice. We may want to take the overpowered option, not because it makes things easier, but because it's how we want to play. But in doing so this destroys challenge, destroys flow, and forces us to feel like we have to choose the other path. So now we feel punished for taking the weaker option. It's this cycle of punishment or lack of challenge that can destroy enjoyment of a game.
The arguments for why you shouldn't be able to join every single guild in something like Skyrim is because of immersion I believe. It feels strange when every group in the game says, "Yeah you can join our club!" When in reality some of these clubs don't get along. Another aspect of it is the feeling of inclusion/exclusion. If you join Guild "A" and you can't join Guild "B" then you are part of something that others can't be a part of. Your character has something that other characters can't have. Of course I've always found exclusive Guilds, Factions, Skill Trees, etc. to be rather annoying. It just limits you, limits your story, limits a lot of things. Sometimes it might not make sense in a world but I'd rather have more options then be barred from something just because I made the "wrong" choice.