Alright, just finished the Thieves guild questline (which was a great story arc), and after completing this, I have to post on here. After aproximately 214 hours of game time, and have now completed all the major 'Guild' storylines, I must say Skyrim rewards you greatly for being bad. Here is why.
The Companions story arc, is okay, with one decent perk which you can chose to keep or dispell, and then becomes utterly useless at higher levels. Also, the storyline is pretty short, and the gear you get is not so great.
The College quest line is very, very short, and the outcome is terribly unbelievable. Let's just say my sword and board Nord got the robes, with not one point in the magic trees....that's lame. However, the lore behind the story arc is worth it if you haven't done it.
The Thieves Guild story line, is awesome! It is full of shady business deals, and has a clever spin that caught me by surprise. Also the rewards are awesome as far as gear that you receive, and you get TONS of gold. So much more than the other 'guilds' reward you.
To further prove my observation, I'd like to point out the Daedra quests reward you with amazing and unique gear pieces, and those story arcs are full of naughty deeds. Also I might point out that the daedric shrines you find within the game are MASSIVE and epic looking, where as when you stumble upon an altar of Talos it is simply a meager statue.
I am about to embark on the DB quest lines, and I am excited indeed. Let's discuss. Do you agree with this? Also, why are the evil daedra gods so massively depicted within Skyrim? If the Nords truly hated the elves, wouldn't they destroy such abominations??
Note: I have played a total of three characters, 2 being good, and 1 being 'bad', so I am basing this on multiple play throughs.