I've been playing the Highborne version of the game and I've been thinking about a plot twist that will happen in a Sentinel storyline, so I came to some possible alternative storyline:
--> How about making Illidan consume the energy of the wells and making him evil instead of Malfurion? Together with his Highborne forces, he could prove to be an excellent distraction of the Burning Legion onslaught upon the Night Elf forces beyond the Mouth Hyjal, which would make a good compensation of the precious time Malfurion lost by saving Cenarius, but he will be extremely hostile towards Malfurion. We've seen him using the same fire ability Malfurion is using in the Bad story, so my only guess is Illidan will become just as vile and ruthless as Malfurion was in a Bad storyline.
Now, I won't say exactly from point to point everything in maximum details, just the major plot that I see that may be used as part of the Good storyline. So maybe capturing Illidan instead of killing him and cleansing the foul Corrupted magic he consumed could be a better decision than just straight-forward killing him, which is not what the Night Elves usually do.
--> After saving Cenarius, the demigod decides to leave the group and go help the Cenarian Circle forces, promising to unite his forces with them at the World Tree once his work is done (since having Cenarius joining Malfurion's company would've been too OP).
--> While returning to the World Tree, Malfurion's company will come across many dead Night Elf units and burning/decimated houses of the Night Elf villages, facing many demons on their path. When they finally arrive at the World Tree, they find some dead Night Elf Assassins (or some other Night Elf unit of choice, whatsoever) who would inform them that the base of Night Elves (originally Shalis's base in the Evil story), just in front of Medivh's forces base, is under heavy siege by the Burning Legion (maybe adding a timer to go and defend the base as a main quest?). After defending the base, Medivh will thank them and inform Malfurion the Dragonflights haven't awaken due to Ysera being corrupted by an unknown threat (we all know the threat is actually Eredon's involvement in Ysera's conscience) and therefore hasn't awaken to aid them.
--> Medivh will then send Malfurion to the Emerald Dream in order to deal with Eredon and his illusions (The Eternal Nightmare chapter, I suppose), proposing him to return as soon as possible to defend against the Legion, while Medivh's and Sentinels' (and Cenarian Circle's forces, perhaps) forces will remain to defend the base of the incoming demons. After having a tough battle against Eredon, Malfurion returns back into the original world only to witness the destruction around him. There, he gets informed someone is being captured by the Legion commander (maybe Kazzak or just some random Eredar/Doom hero?). The quest could be to save the captured comrade (held for interogation, maybe) and continue with the quest.
--> If they haven't made peace in one of the previous chapters/interludes, the "Final Conflicts" chapter could be about dealing with both Illidan/Kath'Ranis's forces and some demon forces (maybe with Mother Shahraz/Jaraxxus, like I previously thought about when I suggested making a bossfight "couple against couple", since the dreadlords and Magtheridon will betray the Legion and will not be taken as characters fit for a bossfight), which are spotted establishing a base not far away from the Nordrassil. There could be any character chosen as a bossfight, though, so there would be much space for available combinations.
--> The "Defense of Nordrassil" is the chapter that may look similar to the very first cinematic we've all seen when starting the campaign - Kil'jaeden's full cap of forces advancing to Nordrassil, bent on slaughtering the Night Elves to the very last remaining defender alive and consuming the energies of the World Tree. And the outcome could've been the same had the united forces of Medivh, Furbolgs, Dragon Aspects, Cenarian Circle, the Makrura's faction (the faction the player made the alliance with in one of the past chapters) and the Sentinels not been able to drive the Legion's forces off the World Tree.
Since the main difference of the Good and the Bad storylines is uniting/destroying the forces of Ashenvale, uniting all the factions that could prove to be valuable in a battle against the Legion that Malfurion could come up to is the main goal of the campaign, not slaughtering them. I'd also like to add my opinion on having the possible allegiance with the Makrura faction (and there was one more faction that I forgot about) should be changed from player's choice to an actual quest.
Bearing that in mind, I am sure the battle against the Legion would be very tough, but the united forces will be sufficient to push the Legion back. But the evil doesn't die just so easy. Kil'jaeden's onslaught forces could be used as a distraction, so that Kil'jaeden would be able to slip past the united forces of Ashenvale in order to reach the World Tree.
--> That leads us to the very last chapter "Light and Darkness", which includes our heroes moving inside the World Tree in order to confront Kil'jaeden. Now, I'm not sure which characters could've been used for a bossfight beside Kil'jaeden, since there are many characters that could've lived/died in the previous chapters. But I'm guessing we'll be seeing Queen Azshara again, that's for certain.
And that's some of my general ideas about the campaign. The rest of the ideas I leave for you guys. Generally, there are so many possibilities that could be done. The question is which one would be the most adequate that will cover all the mentioned characters of the lore. Only time will tell I guess