I'll answer a few questions but we can ignore the Kalimdor ED stuff because I just threw that crap in there last minute as a "Well why not?" kind of thing and I agree its a tad stupid.
Why would Genn help Trollbane reclaim a Kingdom that has been lost for over a decade when he still has to worry about reclaiming Gilneas, which is still mostly intact?
I changed it to include reclaim Gilneas as well, Sylvanas is hurting for troops, but not ships if Wrath is anything to go by. Being attacked from both Silverpine and Arathi would be very detrimental to the Forsaken war effort.
Why would you be requesting aid from a human kingdom that isn't even reclaimed yet?
Maybe Stromgarde was the wrong nation, Dalaran led by Jaina Proudmore instead?
Why would we have another Old God in the deeps?
Well there isnt a whole lot of space when you go deep enough, and Old Gods are implied to be pretty large, Yogg-Saron was able to extend his tentacles from Ulduar all the way to Gruzzly hills and maybe further.
Why would Sylvanas go invade a human kingdom that's already under siege from another threat, a threat that could still invade her kingdom?
The Queen's Navy is apparently very impressive in size, but you can't effectively use a naval force on land. By pushing her opponents to battle on the seas she can create an effective barrier at the walls between Arathi and Hillsbrad and the Bulwark at East Tirisfal.
The only way to reach her then would be to secure a beachhead in Gilneas (which apparently the Alliance is very nearly close to doing), or to footslog troops across the Troll lands of the Hinterlands.
Why the hell would the Cult of the Damned work with the Legion?
The demons of the Legion created Necromancy, and the Cult no longer has its King after the death of Arthas. They felt like they were wedged into MoP without a reason because we had already cleared Scolo in Vanilla, but it was somehow still 'there'. I'm not saying Scholo is back, but a small group of cultists hiding in the wilderness of Lordaeron masquerading as a common village isolated from the conflict wouldn't seem TOO out of place.
Where would they even do this in the Hinterlands? There's Dwarves and Trolls EVERYWHERE. I'm sure someone would notice some demons running amuck.
Well Northern Lordaeron isn't possible because of the Faction conflicts, and the Argents presence. The mountains of the Hinterlands are vast (maybe not in gameplay terms) and it would be easy to hide among the mountains so long as you keep a low profile. Nathrezim are masters of deception until its too late. Look at what just one can do to the Scarlet Crusade, or the Onslaught, or the Undercity.
And yes, I agree with you that the Kalimdor segment was just dumb.
But in Cata (and once again this is CATA so we will take everything about it with a grain of salt) apparently the corruption of the Nightmare persists. As you travel through the Dream temporarily to escort Fandral away from Twilight insurgents you are attacked by spawn of the Nightmare. I'm not saying its the best idea. But for Vanilla to build up this big catastrophe in the Nightmare and give us quests for it, only to have nearly all of it resolved in a book was a big letdown.
By giving us a legitimate reason to go there (the corruption persists and the Dreadlords are planning to turn its energy into a portal that could effectively TPK the planet) we can have what could possibly be an entire tier/patch of content.
Azshara wouldn't burst in where there's many different conflicts going on. She'd burst in when there's none because she would want all the attention on her. She's the most selfish character Blizzard has written.
Nazjatar is below the Maelstrom. Where it to rise it would be RIGHT on top of Thrall as he is (or maybe has just finished) fixing the tear caused by Deathwing. Were is to rise he would rush to make a call for heroes, and we could develop the fate of Kezan and the South Seas as well.
And if Azshara herself rose her capital from the sea, then she quickly would become the focus. Im not saying we devote an entire expac to the Dream, that could be a patch that would be an in and out quick band aid fix, just in time for Malfurion to return to Azeroth to face Azshara.