The choice between Stormcloaks and the Imperials is supposed to provide a little more immersion in the story: you choose a side, and while both sides have comparable quests, they take on a different flavor and will have different actors.
To this end, both the Imperials and the Stormcloaks have and 11-part quest chain concerning the Civil War that ravages Skyrim. The first few quests are almost identical, but then they branch off as each side wins (or loses) major fronts in the war.
And in general, choosing one side or the other makes things easier for you if the side you chose is in power.
For example, if your side controls a major city, you generally don't have to do any special favors for the Jarl in order to get permission to buy a house: it'll be given as a gift for siding the cause.
But the Elder Scrolls series is all about choice, and you're not going to be limited much by what side you choose. Choosing the side you most identify with will generally work out just fine.
But fear not, you didn't make a permanent choice when you went with Ralof (the rebel). You'll be able to play both sides until the last possible moment. You don't seal the deal until you swear an oath to either side by going to their stronghold city.
Additionally, there's one more chance to switch sides during the civil war:
During The Jagged Crown, bringing the crown to the opposing side's leader will let you turncoat and join the other side.
One of the footnotes on Joining the Stormcloaks (UESP) reads:
On the PC, it is possible to use the console to advance through the quest by entering setstage CW01B stage, where stage is the number of the stage you wish to complete. It is not possible to un-complete (i.e. go back) quest stages.
(Emphasis mine.) Looks like you're not a true brother or sister of Skyrim.
However, if you have a save from before using the console (always a good precaution, but not one we always remember), you could try going back and instead of advancing the Stormcloaks questline, advance the main one. You may miss a bit of content, but at least you'll be able to do both.
To skip past talking to Ulfric, use setstage mq302 30. Alternatively, just complete "Joining the Stormcloaks" (and possibly also "The Jagged Crown") so that Ulfric will stop acting like your mission commander and start acting like a leader at a meeting.
Source: http://www.uesp.net/wiki/Skyrim:Season_Unending#Bugs
Best Answer
Imperials and Stormcloaks both have hidden crime faction ratings that track your crime against them.
In order to reset your crime rating with each enter the following commands into the console:
Imperials:
Stormcloaks: