To play devil's advocate because I feel like you got some half baked ideas.
Why doesn't the Alliance use the Vindicaar?
Prophet Velen is in charge of that weapon. He probably isn't the type to just nuke a capital city because of the leader and kill thousands of innocents. They would be no better than Sylvannas at that point.
If Jaina can make ships fly why doesn't she fly the whole fleet into Horde capitals?
I imagine she has limitations in her power. That is a lot of ships to fly into an area. Not to mention both sides to have flying ships to deal with that.
Why doesn't Jaina or Magister Umbric use teleports/portals for massive advantage? Or Dark Iron mole machines?
Probably because the Nightborne would also have capabilities to sense that kind of magic being used since they are also pretty attuned to magic.
Why doesn't Khadgar (or any other neutral leader like Hamuul Runetotem, Alonsus Foul, Meryl Felstorm, Alexstraza...) slap the hell of Horde leaders for starting yet another war? Or at least don't act as a neutral party for negotiations?
That wouldn't make them neutral then would it.