I'm playing the game without doing the main quest, dragons are worse than roaches. I want to buy the house in Windhelm but to do so, I have to complete the civil war on the Imperial side since I don't play to side with the stormblokes.

So my question is, does doing the civil war quest line make any significant changes to the game? Will the changes in leadership alter the available quests in the different holds? I know you don't have to do the peace talk when you do the main quest. Do the same people take over as Jarl for those cities?

I just want to know what I'm getting into before I start a war.

The guards will wear a different color uniform, and the Jarls will change in some of the towns.
You should still be able to get all the houses unless you encounter a bug, but some quests may be unavailable.

That's the main thing I was wondering, I want to do as many quests as possible beforehand if they're going to be unavailable. Does Maven still take over Riften and so on?

Yes, she'll become the Jarl if the empire wins. I heard that she may become Jarl of Markath depending on the negotiations during the main quest.

You'll probably want to do at least the Skooma-busting quest, Blood on the Ice and the Forsworn Conspiracy before concluding the Civil War.

To quote the Who, "Meet the new boss, same as the old boss". For the most part, it just changes the "flavour" a bit. The Jarls get replaced (except Elisif), and the Guards in former Stormclock regions get replaced by Imperial soldiers (and vice versa).

Maven takes over Riften if:
-You do the Civil War Imperial quest and liberate the Rift;
-You don't take sides, or are doing the Imperial side of Civil War, and give Riften to the Empire during MQ Season Uneding;
-You are doing the Stormcloak side of the Civil War, and do MQ Season Unending. (The Empire auto-takes Riften.)

Note that being neutral or Stormcloak at Season Unending allows you to change this jarl again.

Just to let you know that the empire is weak and ridiculously pathetic.

Sure beats racist Thalmor puppets if you play a beast race.

LOL The beast races are racist Thalmor puppets. Well, the Khajiit definitely are. The Argonians are racist and possibly in league with the Dominion when it suits them.

Technically the imperials are thalmor puppets aswell, although Ulfric is more so as he is unwittingly helping them

Yes, yes everyone is racist but I meant between the Empire and the Stormcloaks. The first time I walked into Windhelm, the decision was made.

Anyhow, back to the topic at hand.
Basically the game is the exact same and the quests are too, no matter who rules each hold?
Or should I do every available Jarl quest/become thane of every town before starting the war?
I simply don't want to miss out on a bunch of potential quests just because of one choice.

If i remember right the new jarl will make you thane after they take over, can't remember if they still offer the quests or not though, i say do them just to be safe. EDIT not sure why that quoted twice but fixed now

Doesn't make the slightest bit of difference. A couple of guards say thank you, but I still run into Imperial and Thalmor Patrols leading Stromcloak prisoners, everyone, townspeople and guards still talk about the problems the war is giving them. The only thing that has less of an effect on the game is killing the Emperor.

The look of Whiterun will change a bit.

Thanks for the assistance, going to mop up some quests now.