"In addition, instead of right vs wrong, there's often wrong vs wrong, for example choosing between letting an ancient tree die vs infiltrating the sanctuary of the "mother" tree to provoke it by stealing sap (and thus getting people killed)."
Just wanted to update this--although I stand by the original statement, I found that this particular quest
bugged for me. Apparently, you're supposed to get an npc approach you and offer you an alternate route for reviving the tree, but in my playthrough, this never happened (BECAUSE BETHESDA).
I also wanted to add that apparently by not choosing sides in the civil war, I missed a great deal of the plot. However, it looks to me (I researched both sides online) that taking sides and progressing down the quest line forces you to betray characters that have staunchly supported you, even when your requests seemed bizarre.
Therefore, I suggest that if you're going to take sides, that you do so asap, and complete the Civil War bit before becoming attached to any npcs. See, as faction X (whichever you choose) progresses in their consumption of Skyrim, they will replace the Jarls (local kings) and ruling families with their own choices. These new npcs will supposedly behave exactly as the old ones did during other quests, though, meaning it'll be the new ones you'll get help from & make friends with, rather than getting to know the originals only to betray & replace them.
There's a very nice house I want to buy, but aside from it being bugged all to hell (the weapon racks are known to not work, and display cases can "devour" whatever you put into them), you also need to get halfway through the civil war questline to buy it. I'd rather just... not. I guess it's a good thing that the immersion is enough that I don't want to betray the npcs who've helped me out, but on the other hand, politics = depressing, and I don't like my fantasy games to be depressing