Ignore the history, intention, truth or whatever reason behind this war.

Just base on what you can see after the civil war, who do you think is doing better job?

For example, I side with Legion and in my opinion:
- Brina becomes Jarl of Dawnstar. Good, because she sounds more rational.
- Siddgeir remained as Jarl of Falkreath. Bad, because he milk-drinker bastard. However Dengeir is a paranoid.
- Igmund remained as Jarl of Markath. Good, because Silver-Blood family treats people as slave.
- Idgrod remained as Jarl of Morthal.Bad...well, she is not a bad person but I don't think she is a good Jarl.
- Maven become Jarl of Riften. Absolutely bad! She is a [censored]!
- Balgruuf remained as jarl of Whiterun. Good, because he is my favorite character
- Brunwulf become Jarl of Windhelm. Good, because other races will have better treat.
- Kraldar become Jarl of Winterhold...or not? Anyway it is good because he sounds more rational.

5 good VS 3 bad, I think I made a good choice

Honestly, there is practically no difference when the questline is over. The only difference is the Jarls. I can't remember all of their names, but for me, just keeping Maven Black-brier from being Jarl makes up for everything else. Laila Law-Giver may not see some of the corruption in Riften, but she truly cares about the people.

The only replacement that made me sad was losing Balgruuf, but he made his choice. And the guy who replaces him isn't too bad.

The other one that svcks is the Jarl of Dawnstar. What an idiot.

Dengeir of Falkreath is actually a pretty good Jarl, when it comes down to it. He is slightly paranoid, but as he says, at least he doesn't use up all of the hold's money buying crap for himself. So that's a plus.

The Jarl of Winterhold is kind of adorable, so I'm happy to keep him. "I don't care how many colleges they build!!" My first duty as guildmaster will be to build five more colleges, all surrounding and enclosing Winterhold.

This is a pretty big spoiler, but at the end of the questline Elisif remains Jarl of Solitude. Ulfric says that if she swears fealty to him she may keep her position and she accepts. So hey, that's good, she's cool.

Markarth. Eh. Both of the Jarls svck equally. I guess the Silver-Bloods are, like, SLIGHTLY worse.

Morthal, blah. Their Jarl is basically a less-mystical replacement of the current one. Positive? I dunno.

And then we have Ulfric. Hells yeah. Keeping him is a positive thing.

So, it's really hard to calculate since to me many of the Jarls are similar. I do love Brunwuulf of Windhelm. If I had my choice I would make him Jarl of Riften, and make Laila Law-Giver Jarl of Dawnstar and boot that jerkwad out.

So there's 5 positives, two "mehs," and two negatives for me. I did the imperial line as well in the beginning, and to me, having Maven Black-briar be Jarl of Riften KILLED it for me. Never again.