As long as the Warcraft Universe makes sense within itself and follows its own rules, I dont much care how ridiculous things are. Its supposed to be fantasy and thats basically what it is.
Anything that doesnt make sense can be explained later in a book or comic and It'll be fine with me. I dont like that the context that makes stuff you see in-game make sense is often left to the other forms of media, but thats an entirely separate gripe.
I dont think its necessary to call characters like Jaina a mary-sue. It may seem like Blizzard make their major characters stupidly more powerful than they should be, but you might be looking it the wrong way. They arent written OP because they are major characters; rather they are major characters because its apart of their story to be that much more powerful.
For Example:
1: High Elves taught humans magic and they noted that humans seemed to have an affinity for it, picked it up quickly and I'm pretty sure its mentioned somewhere in the lore that they are also able to generate more force/power than a similarly powerful elf mage could. (I cant back up that last point though)
2: Jaina was a prodigal student, was chosen to study under Antonidas; the leader of the city of mages. She was also mentored by Aegwynn in Theramore.
3: Jaina was apparently magically supercharged by the Mana-Bomb at Theramore, further increasing her power.
4: Jaina had her staff supercharged in the Throne of Thunder, further increasing her power.
5:Its very common in WoW for mages and other spellcasters to 'enchant' objects with magic, causing them to do a function seemingly on their own(brooms, flying discs/carpets, etc). In the cinematic the only spells you see Jaina cast are the blight freezing halo thing (which btw isnt even the first time magic has been used to destroy/disperse/neutralize the blight), and when she turns the ship. Unless its specifically stated elsewhere it seems perfectly within the rules of WoW for her to have enchanted the ship to fly itself since she doesnt appear to have to channel any spell to keep it flying. Likewise the magic shooting magic cannons could be explained the same way, as being enchanted to fire arcane-empowered projectiles at her command.
With that in mind I can accept that she had prepared her warship well in advance. She would have enchanted the ship to be able to levitate on its own and enchanted the cannons to be magically empowered and able to fire on command. That way she is free to cast her magic as needed and she can simply nudge the ship in the direction she wants to steer it, which we see her do in the cinematic.
Like others have said this is well within the bounds of WoW canon considering the other things we have seen mages capable of doing with their magic. (flying cities, portals, conjuring objects, enchanting objects, enslaving elementals, etc)
The other main point is that the 'main characters' of the story are there because they in most cases are the best of the best in their field. This is either because they were naturally gifted and rose to the top of their civilization because of it(Malfurion, Tyrande, etc), or because they were born into leadership and were thus trained their entire life to fulfill that duty (Anduin, etc).
On top of that a lot of them have experienced things that would further increase their magical power/fightning capabilities/political & tactical prowess. Its not ever really brought up in game because big lore characters are given a backseat to the 'player character' who does all the menial tasks, but it is mentioned in the other media that during a lot of the time we spend doing the quests/dungeons/raids lorewise those major lore characters are doing their own things too. The world (of warcraft) keeps spinning everywhere even when the player isnt there. These characters spend their time looking after their peoples and training to become stronger when we arent around.
Anduin is a great example of this. Its brought up a few times in various books and comics that he has been destined to rule since he was born. He is after all the first born son of a king. While in game he just stood there in the keep waiting for alliance players to hand him quests or horde players to come fight him, in the lore he has spent all his life training and studying to be a king. That means training to be a capable fighter in multiple forms of combat and studying the tactics of war & politics. He is young and the writers often make a point of it when he talks to the other Alliance leaders. They obviously have more experience than him, but its not as if he has been lounging around with his thumb up his ass his entire life either.
So like I guess TLDR: I too enjoy the fantasy and am not really bothered by any of the things people seem to be getting annoyed at.
But maybe im just a dirty fanboi who is blinded by hype and autism which makes it feel like everyone on MMO-C hates everything about everything.