The problem the Alliance has is as simple as the statement at BlizzCon that the Alliance is the 'Captain America' faction, the faction that has a more standard heroism about it. The problem with that is, in many ways heroism is depicted as being reactionary. You respond to a threat, you react to a crisis, whether it be Deathwing or Garrosh. Villains act, and heroes react - it's one of the reasons that actors often state that the bad guy is more fun to play. For better or for worse, the Alliance presence in Pandaria was a reaction to the crash-landing of Anduin's ship after it was chased by a Horde fleet, and everything that followed was reactionary. The Alliance stayed in Pandaria purely because the Horde was there, they weren't there to explore or even conquer. The entire struggle over the Divine Bell was a struggle to keep the Horde from getting it because they knew the Horde would use it (as they did) and so far, despite her having every reason to feel that the Horde cannot be trusted Jaina Proudmoore is being painted as villainous for maintaining this position.
Frankly, would you believe in someone who went from the source of diplomacy to the aggressor (and keep in mind, Jaina actually tried to keep to the diplomatic path as leader of the Kirin Tor even after Theramore was destroyed, only turning from it when she discovered that the Sunreavers had aided the Horde in stealing the Divine Bell) if she was so easily mollified? The people who now stand in control of the Horde were there underneath Garrosh when he destroyed Theramore. She'd have to be a fool to trust them. Frankly, what the Alliance needs is more Jaina Proudmoores, and for them to be taking actions. You can make the argument (and I certainly would agree with it) that attacking the assembled Horde leaders in Garrosh's throne room and dismantling the Horde absolutely would not have worked, for both lore and gameplay reasons, but acting like it's not an understandable impulse is disingenuous.
Going into Warlords of Draenor both the Horde and the Alliance are acting in a reactionary manner, responding to the threat that the Iron Horde poses. But once they're there, it'd be nice to see the Alliance acting proactively, not only taking the fight to the Iron Horde, but perhaps going even further. Imagine Alliance attempting to make alliances with the native ogres or arakkoa in an attempt to pen both the Iron Horde and the New Horde in? But also, I'd like to see them do things that have nothing at all to do with either Horde - why not do some exploring of ancient ruins, or set up an expedition on the oceans to go to places like that mysterious southern continent.
In fact, this could be extended back to Azeroth as well. It's time for the Alliance to take chances and do things. These don't always have to work out in their favor - a defeat can be as good as a victory, as long as its not a defeat that causes exact symmetry in the other faction. These need to be stories that deal with and establish the Alliance character as actors, not passively waiting for events to respond to in some fashion. Think about when the Explorer's League would send Alliance players into places like Uldaman or the players would take it upon themselves to raid Molten Core - there was no overarching factional conflict motivating these, and there doesn't need to be.
This is the main issue I see for Alliance stories going forward, and since we started off by defining the Alliance in a comic book way, I'll use a comic book story to explain it. One of the better stories of the 1980's was a 12 issue limited series named Squadron Supreme. In it, a group of super heroes found their world devastated after a villainous calamity, and rather than simply return to the status quo, they chose to be proactive. It didn't work out as they hoped - in the end, they went too far and had to come to terms with their ambition overreaching their ability - and it's exactly that kind of story that the Alliance needs now. We need to see the Alliance do something. Does it have to be successful? No. In fact, it being unsuccessful and causing more problems than it solves could in fact be great for the setting and its overarching story, showing that in the world of Azeroth and beyond it's no longer possible for these two factions to act independently of each other. That they always have to take each other into account. But whatever happens, we need an Alliance that acts, and is not merely acted upon, an Alliance that makes things happen.
Captain America needs to throw that mighty shield once in a while.