What to go for next? Companions, assassins, imperials/rebels or the main quest? Dark Brotherhood seems the best choice for a bounty hunter wannabe, but I'm unsure if that questline overlaps with other questlines.
At least in my game, I haven´t encountered any conflicts caused by the Dark Brotherhood questline.
For what it´s worth, I´ve finished all questlines in the game and Dark Brotherhood belongs to the better ones the game has to offer, I think.
Characters involved are a bit more fleshed out than usual, there´s a lot of references to DB from the previous game which give it a good sense of continuity and it has well balanced gameplay elements, aka half or more of it doesn´t involve hack´n´slashing through dungeons (for example, inclusion of the Bard´s College was certainly a nice touch, but, man, were the quests for it lazy) and some rewards are pretty cool. However, personally I´ve found the plotting to be so so and one of the rewards ends up being annoying due to a certain much needed feature missing.
Still, I think it´s the second best guild after Thieves Guild (which has most content and most "guild-y" feel) and is much better than Companions or very lazily put together Winterhold College (whose questlines are very thin and completely lack any sense of "guild-y" advancement).
Imperials vs. Stormcloaks is in my opinion well conceived only as a setting and as a "gray choice" feature, the actual quests themselves are nothing to call home about and consequences aren´t all that substantial, though it´s cool Bethesda implemented this kind of exclusivity into the game nevertheless.
Also, note that these questlines potentially conflict with the main quest, I´ve posted about it in the bug thread.
Main quest is pretty run-of-the-mill as well, there´s a promise of intrigue about 2/5 into it, but that proves to be false fast and it´s simple and nothing special afterwards. Not really bad per se and the ending is rather nice/cool (but has barely any effect on the world), but in my opinion it´s a lot less interesting than, say, Morrowind´s main quest.
Anyway, got a bit carried away here
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