I will start by saying that all this happens very similar to how Batle of Undercity happens though phasing. I am in no way endorsing the complete deletion of the vanilla instances and areas. Also this is asuming the Cataclysm IS the new expansion as far as rumors go. And please dont flame about Cataclysm "leaks", do it somewhere else.
So the whole story starts with the whole Cataclysm thing.
We do some long quest chain to help some guy (lets call him Bob) in fixing Azeroth. You do this by doing good stuff like killing demons, collecting elemental shards, etc... The final quest is the Attunement to the Core MarkII so you can get attuned to the "new" Molten Core wich is a 5man dungeon similar to Eye of Eternity.
But the instance is obviously dead, you see it changed abit with new lava flows, some fire imps may lurk around. There are almost no mobs but the dangers are the periodic lava flows, rocks falling (like Sartharion fires?) so you need to survive to the end.
You escort Bob untill you reach the chamber of Ragnaros. He tells you that he needs some stuff from Majordomo's corpse but in fact he actually summons Ragnaros again. Here you see a very cool Ragnaros spawning cutscene like the Hammmer glows and fire bursts out of it reigniting the Living Flames spawning Ragnaros. Bob does some spell, yells "I got what i wanted, so long suckers!" and teleports out leaving you with a very pissed boss.
Now you fight him and upon death Ragnaros is very angry and summons alot of mobs into the instance saying "I MAY PERISH FROM THIS WORLD BUT I WILL TAKE YOU WITH ME, INSECTS!". You have to kill those mobs on your way out. Did i mentioned that lava is coming out and is filling the instance so you need to get out quickly before you are engulfed by it! The last miniboss is a reignited corehound that gives the loot.
At the end you get the instance portal to Blackrock Spire. There you kill the keymaster (he is right at the start) to be able to open the door from inside because there is now a door to enter BRS, its phased so lowlvls wont see it. Only 1 key drops per kill so ppl roll on it. When you get the key you can open the door to Blackrock Spire.
Blackrock Spire instance is practicly the same with some differences. I dont know about the lore of Cataclysm so ill asume that the new dragonflight that Deathwing is creating (the successors to the failed Netherwing) are the ones in this new BRS so ill call them "Obsidian". This instance (you start by going LBRS) is timed so that you need to reach the final boss in X minutes before lava gets there. If the timer finishes the boss starts moving up running away from lava and you will fight everything that stands inbetween. This is hard mode if you do this way and you can activate the lava flow sooner by using a thingie in there. When you beat the last boss you need to go up and up (now you go back and past the old door to UBRS).
At the start of BRS - URBS is blocked by fallen debris and only after lava starts flowing there is a quake that shakes it and frees the path up to URBS. When the path opens up you go up and avoid steam geysers, falling rocks in a race against the lava up to Pyroguard Emberseer's room, there you are protected by the remaining leftover magic field from when you killed him back in the 60s. Now the path is blocked and the only way is to go up. The instance is also quite in ruins compared to vanilla one, here you fight mobs and do things acordingly to lore. Since i dont know the lore ill asume that your faction has some "front assault forces" inside BWL in order to attack the whole Deathwing stuff going inside. Your job is to reach them and help them. A couple of bosses here and there, but your path isnt the same as before. This time you dont go into General Drakkisath's room, instead of you go straight to Blackwing Lair zoning portal.
In Blackwing Lair(10/25man), in Razorgore's room there is a NPC quest hub that gives teleports in and out and is battling the new dragonflight like "we dont know where they came from, we had scientists working on the stuff when out of nowhere these new dragons came from Nef's balcony and killed everyone. We managed to hold them here but alot of our stuff was left behind".
The bosses are these:
1st - You help Alex reviving Vaelstrasz. You fight some leiutenant from the Obsidian dragonflight + adds. At the end of the fight Alex finishes reviving him. This is major lore stuff to geek on with some dialogs between the eversexy Alex and Vael. She says "sorry couldnt help now i revive you, world is in danger", vael replies "yeah thanks but i owe these heroes and will help them on their quest". Now Vael in human form helps you though the rest of BWL.
2nd - In the old Suppression Rooms there are 3 minibosses that the raid must split between to kill at same time, the first has more health but the others are further away. One of them is tankable by a ranged so no need to bring 3 tanks. The point is to kill them at same time and manage the supressors so its tricky.
3rd - Broodlord Lashlayer got revived and he is Obsidianish now (imbued with the new dragonflight's strenght). He goes like "Why do you insist in remaining here? Her Highness personally oversees this operation and as Broodlord i will not allow you to proceed and destroy all that she worked for all these years." Upon reaching 75% health he says "This time i will not be alone, your previous battles mean nothing!" and he summons the 3 minibosses you killed just before. This adds a soft enrage timer while the 3 minibosses get to you (the supressors work on them).
You can opt to get rogues disable the supressors initiating the hard mode (or just letting them join the fight). You must kill them before Broodlord dies. Each time you kill one of them he says "No! I will not tolerate the death of my brothers, you will pay!" and he gets a buff that puts a HoT on him and increases his damage. This becomes a DPS check to outdps his HoT + it stacks with 3 minibosses dead. You still need to kill them if you opt to kill Lashlayer before the minibosses are dead (loot similar to sartharion).
4th, 5th and 5th - id leave these for new lore figures. Tbh i wouldnt include the drake trio Firemaw/Ebonroc/Flamegor. They are realy dead, not revived (too much recicling ftl) and leaves space for new lore. Also trying to invent new tactics for these is kinda pointless so we skip ahead.
6th - You get some serious trash pull here (like pre-Vezax). At the end Lady Sinestra (oh yeah!) appears and goes like:
#Sinestra: "Damn you mortals. Your kind is realy a neusence! Not only you thwarted my son's plans but now you come here again to delay my work? Yet even after his failure not all is lost... You see, by continuing his work and, no thanks to you, I was able to finish His new dragonflight myself.
#Vael: "No! This should not had happen! Your plans are as horrible as the scourge, a corruption of life! I won't let you--
#Sinestra: "Shut it little one. You failed to best my son and now your arrogance will be your downfall again. Do you think you can beat me? Then come and visit me at my son's grave." (she walks back)
This spawns a new badass Obsidian Bob (hell yeah, he's back!) so you fight him after a brief dialog.
This should be a very complex fight with lots of things going around, debuffs to cleanse, positioning, etc... A very fun encounter to be remembered. This will test the skill of every raid member
7th - You walk into Nefarian's balcony, you see his corpse above his old throne, headless. Sintharia (Lady Sinestra) is in the middle and talking to Mr. Deathwing himself that is hovering in front of her outside:
#Deathwing: Are those mortals also part of your plan?
#Sinestra: It seems they defeated our Prime, but our plans here are complete.
#Deathwing: Very well, return to me so we can continue to the next phase.
#Sinestra: Yes, after I deal with these slimes myself.
#Deathwing: I know who they are. I sugest you return immediately, don't underestimate the slayers of Old Gods. (he flies away)
#Sinestra: Slayers of Old Gods... (she walks to nefarian's corpse) I guess my son wasn't such a failure after all... Fighting you would be too much for a single dragon to handle it seems. (she transforms into dragon)
#Vaelstrazs: You won't get away this time Sintharia!
#Sinestra: Realy? And who will stop me, you? Don't make laught. You--
#Vael: I WILL MAKE YOU CRY!
He transforms into dragon and charges her. Now the two dragons fight outside while Bob with the whole "Tempest keep was merely a setback" style attacks the raid. Here Vael gives you Essence of the Red so you can have some fun killing Bob rather quickly (he has a 2-minutes enrage timer, 45-seconds for archievement) and start DPSing Sinestra, but after a few seconds of that she knocks off Vael down back into the far side of the balcony and flies away. A loot chest appears now.
A red drake arrives like "vael was taking long so alextrazsa asked to see whats going on" and you talk to him to get a flight back into Searing Gourge (alliance) or Burning Steppes (horde) zoning you out of instance.
I dont want it to go like the new Onyxia "zero lore, maximum fun". There is so much possibillity to reuse old content with new spinoffs without hurting the vanilla even for those rerollers that want the old 60s by turning XP off.
Im not a huge lore nerd but i hope this makes sence (if i made mistakes about that please coment).