Hello, I'm new to the Elder Scrolls series and quite new to Skyrim. I've only been playing it for about a week, and am having a blast. Well, I am now. Some lady in Whiterun said something like "I'm married... but I guess you have other things on your mind," so I got mad and killed her, got jailed, killed, and I went back to my last manual save. Of course I was only renting the game then, so I quit, but bought it last weekend and ended up back in jail with all my progress and now I'm having fun again. But I severely digress.
I noticed something odd... the game has a very large focus on evil. You can join the Dark Brotherhood or destroy them, but if you destroy them you don't get anything, and if you join them you get a lot. You can also join the Thieves' Guild, but you can't destroy it. There's also a ton of Daedra quests that have you doing evil things.
Why are there no good things? Why isn't there a reward for being good? Shouldn't there be two sides to the coin? I'm just wondering, because I'm not one to partake in these things (especially the Dark Brotherhood).
There are good things to do as the Dragonborn. You can help people in the nine Holds, and be rewarded with the title of Thane in each region. You get rewarded for helping people finding stolen or missing items, or resolving disputes. You can give money to random encounter farmers who have lost everything. You can stop threats in Skyrim. You can be proactive and investigate a murder, stop an attempted murder, and help one side in a civil war between two factions that are lead by flawed (but well-meaning) leaders who are both trying to do what they think is best for Skyrim.
Some quests do make you question if it's good or not, and it depends on your own morality: you can meet an old Orc who wants to die an "honorable death." Is it good to grant him what he wants, or is it good to leave him be, even though he wants to die as tradition demands? While some Daedric Quests can be seen as evil or good, some do leave it up to you to determine their outcome: Is it good to return the Star to Azura to create Azura's Star, or to help Nelacar construct the Black Star because of his arguments about the nature of the Daedric Princes? There's also the demand made of you by the Blades, which is another dilemma that focuses on your own morality, and whether it's right or wrong.
I think the College of Winterhold is fairly good, although the narrative is geared towards a mage-centric character. I never really felt like an evil character would fit the narrative, given who you encounter at certain times. The Companions is geared towards a warrior, especially in terms of the negative view some of the Companions hold towards magic and mages, as well as the negative view against stealth combat, but I think it's another good faction; the members of the Circle in the Companions are also made up of people who are divided on a "particular issue," but overall they help people and are highly regarded by the people of Skyrim.
As for some quests focusing on being a "bad guy," you aren't forced to engage them if you don't want to. A good character can leave the Thieves Guild in disarray, destroy the Dark Brotherhood, refuse to engage the Daedric Princes he (or she) thinks are vile (like Molag Bal), helping end the civil war, and stopping Alduin.
I like that Skyrim allows me to have a proactive character, which was an issue I had with Dragon Age II, where I felt very railroaded by the plot and unable to do a lot of things I wanted to. In Skyrim, I have a Tribunal mage who tried to do what was right: my Dunmer defied Azura (as he shared Nelacar's views), helped the people of the nine Holds, helped his fellow mages (and even some random ones that sought him out), stopped the Thalmor, and never engaged in the "dark" quests, while I have another character who became a member of the Thieves Guild and the Dark Brotherhood. My point is that there's room to do both, with seperate characters, or stick to one type of style if you would prefer. Simply because there are quests that can be viewed as "bad" doesn't negate the fact that there are also "good" quests that reward you as well.