Malfurion cannot be part of the current story for a various amount of reasons.
First of all, many people misinterpret the Night Elfs from the start. Night Elfs despise conflict.
Here's a little summary taken from the wiki:
That part in bold shows how there's a natural resistance within the NElfs to even take part in the "lower" races conflicts.Virtually all remaining night elves consider it their sworn duty to maintain the safety and balance of the natural world. They are generally honorable; a strict but just and truly compassionate people. Even so, they tend to be dismissive and distrustful of the younger races they now find within the world, and whom they consider to either be living in stubborn ignorance (for war-mongering and the destruction of nature), or as too short-lived to ever attain the responsibility and wisdom which the night elves have gained through their burdened past. In turn, many of these younger cultures perceive the night elves' attitude as one of mere arrogance or of superiority. The night elves tend to be looked upon with awe, wonder, and even mistrust, if not for their shadowy and secretive nature, longevity, and ancientness met with youthful appearance (they look forever young), then for their aloof and judging demeanor
The cataclysm was an event that greatly impacted them directly, even to such great extent that Malfurion had to be brought back.
For himself, he cannot be part of the last stage at all. For one reason alone. Garrosh is no match to him at all. We wouldn't have a Siege of Orgrimmar raid, since Malfurion would be perfectly able to take care of Garrosh without anyone's support other than his own powers and the forces within his powers.
And here is where we can argue about lackluster story telling in the game.
For once, we can use the Nightelf aversion of war conflicts, since it destroys nature and balance within. But where does that stop? When is enough enough?
No other race in the game suffered more from the Cataclysm events than the Night Elfs. No other race suffers more through Garrosh's doings by using the Cataclysm to his advantage and ravaging the Night Elfs most sacred and ancient territories.
By any logic means, the threshold for retaliation has long been surpassed. The Nelfs striking back and crush Garrosh's forces is past overdue.
Certainly, the Night Elfs cannot defeat the Horde as a whole, all on their own. But they'd certainly have the powers to drive the Orcs out of Ashenvale without much problems at all. Garrosh's invasion of Ashenvale makes in that regard zero sense. Invasion due to the natural disasters, yes... But certainly not the extent which is seen in the game.
I strongly hope that the race gets some center stage in the next expansion.