I just wondered... I'm following the main quest I have been taking my time with it on one character so please don't post any spoilers beyond where I am at the moment.

Basically I've reached the point where I have to convince the Jarl of Whiterun to let me catch a dragon and he wont do it unless I can get the stormcloaks and the legion to come to a truce.
I have completely avoided taking sides on the civil war on this character and I got thinking if you join the stormcloaks or legion does it mean you get different options here I know if you follow the stormcloak questline you eventually take over whiterun.

Basically I'm interested in knowing what happened to everybody else when they got to this point? Especially if you have done the civil war quests along with the main quest. Thanks.

I've never done Season Unending so IDK what happens there, but once you enter Dragonsreach to start the whole trapping part do not leave - continue until...'whenever'.

I heard that if you take Whiterun and Markarth for the Stormcloaks, if you do the peace treaty, you automatically get Morthal but the Empire automatically gets Riften.

If you do the CW quests, it does not matter who you side with; the reigning Jarl of Winterhold will let you catch a dragon. If you do Season Unending then you have a role-play quest to complete that involves the faction leaders and the Grey Beards.

I have only done Season Unending prior to taking sides in the CW, but I think in terms of the general outcome it always ends up the same way - some holds will be traded back and forth, neither side will be completely happy, but you'll still get your ceasefire.

Which holds get traded back and forth will depend partly on the decisions you make as arbiter of the negotiations, and partly on who currently controls them, which will be different from what it was at the start of the game if you have already joined one side and won some battles for them.

Keep in mind that if you do Season Unending, you will not be able to progress any further with the CW questline (or start it at all, if you haven't already) until you finish the MQ. The ceasefire you negotiated will remain in effect until you are done with the entirety of the MQ.

If you start the CW stuff before progressing that far in the MQ, you have two options: you can put it on hold as noted above by doing Season Unending and then finishing out the MQ first, or you can just keep winning battles for your side until the Jarl of Whiterun (whoever holds that position after the Battle of Whiterun is over) decides that the situation in Skyrim is no longer precarious enough to prevent him from letting you use Dragonsreach. That will happen by default if you finish the CW completely, but IIRC it can also happen earlier once the scales have been tipped enough in your side's favor. However I don't know how many holds you have to take for your side before he will feel it's safe to let you proceed with your dragon-trapping experiment.

Either way, when you do join a faction, you will be taking forts and cities for said faction, until you march on the capital city of the opposing faction and attempt to take it. If you are successful, this will win the war for your side.

The peace treaty negotiation is mostly a matter of who do you want to be Jarl where. If you don't like a particular Imperial-backed Jarl, give his/her city to the Stormcloaks, and vice-versa. It doesn't affect your thanedom at all, not even if you are on the opposite side of the CW from the Jarl. In other words, while the negotiation is interesting, it really doesn't affect the player (other than choosing the CW battle locations). If you haven't joined either the Legion or Stormcloaks, no worries. If you have, still no worries, just more smart remarks from your commanding officer and the opposing side.

It's a pity that there are not more consequences to your actions.

It doesn't matter who is Jarl of Whiterun - the MQ will proceed on the same conditions regardless.

Hmmm... Yeah kind of a dissapointment. I hoped there would be more consequences for the players actions in this. So if my character had chosen a side on the CW and had taken all the holds I would still have to have the the peace talks O.o I don't think my Nord stormcloak would do that, she's more into bashing imperial heads in with a warhammer than talking peace... That svcks.

Uh... no. The whole point of having the peace talks is to arrange a temporary truce so the Jarl of Whiterun doesn't have to worry about you luring a dragon into his city AND the threat of Imperials and Stormcloads trying to use his hold as a battleground.

If you join a side in the war and take all the holds for your side, the war is over, done, finished, and no truce is necessary (or possible). The Jarl of Whiterun no longer has to worry about the war so he will not require you to negotiate a truce before he agrees to your request to use Dragonsreach and Season Unending will never happen.

Season Unending only happens if you are playing the MQ and ignoring the war completely, or if you start playing the war quests and do not finish them (or at least tip the scales far enough in your side's favor) before you get to the point in the MQ where you need permission from the Jarl to use Dragonsreach.