For Whiterun, you attack the city and then tell the Jarl to leave. Or in the case of the Empire, you defend it. Why is it only Whiterun you can attack? Why am I stuck attacking lousy forts? If I take the fort over, shouldn't we march in the city, go where the Jarl is and force them out and watch the new Jarl be seated? I was kind of disappointed in this. Any opinions?

Because your not necessary for every major battle, by securing the forts your faction is thus able to secure the hold.