@Fluent and wolfgrimdark
In that case, GTA is the most amazing series for roleplaying ever made. Side quests all over the place, and you can choose to turn down as many as you want.
Sorry if I'm being a bit snide here, but please point out a game which has side quests, but you can't skip them. Or maybe find an RPG that does not have side quests at all.
Like I said - apathy is not the path of a good guy. Apathy is evil, or neutral at best.
So explain to me why a "good guy" would track down the Shrine of Boethiah when the book itself states that a man killed another man in cold blood to gain the favor of Boethiah. Is a good guy going to say "yeah, that's something I want to do! In fact, I'll do it in a good way, and bring down Boethiah instead!" Do you know putting in those types of choices would easily have doubled the amount of content they'd have to make for the game. It just isn't feasible.
Instead they give you the option to use your own moral compass when choosing which things to pursue. I personally will ignore Boethiah's calling, because it sounds like bad news to my character. Maybe when I get curious later on in the game I will check it out, but even then, if the quest is too "evil" I will turn it down. This is also good for replayability. I'd rather be locked out of content as a "good guy", and revisit certain quests as a "bad guy" with another character, and the content will all be fresh and brand new to me.
I don't see the big deal here. You have the choice to follow through on what you want to follow through on. That's the best choice you can make. You choose to serve the Daedric princes and do their bidding, but at what cost to your own morality? You can choose to join the Thieves guild, who are looked upon as scum, and you choose that shady path for your character. There are very real roleplaying consequences for making those choices, and even direct rewards, for example, you get access to the shady, "evil" content. If you don't want to pursue evil content, you don't pursue it. You are always making those types of moral choices in Skyrim.
Again, this is another design decision Bethesda made that is simply different from other approaches, not worse. It's just different. Your choices are more about the actions you take and what things you choose to pursue, rather than doing every quest and having your choices of how to finish the quest. Yet the game even has some of that type of roleplaying as well. I've had quite a few quests where I had a choice of which way I wanted to complete it.
And the reason you have to kill the bad guy in most quests, is because Skyrim is a harsh place, and the outlaws and evil people of Skyrim do not respond to civility, they respond to violence. Marcurio will tell you that when you encounter necromancers, or vampires, bandits, etc. These aren't people to be reasoned with.
But in bottom line terms of "does this game satisfy my role-playing?", I give a resounding YES. What it lacks for options during quests, it gives you options to pursue different storylines in order to shape the overall picture of your character and his morality and personality. The main point I'm trying to make is that Bethesda lays out these storylines which give you the choice of completing them or not and shaping the moral outline of your character. That's the best way I can explain it. It still might be vague though, but I see some people know what I'm trying to say.