However, in my estimation difficalty is too easy - i know that warcraft 2 had no normal AI, and in some missions its nesseserry that enemies don't react when you destroing their base, netertheless - it is too easy (in original WC2 - it feels OK just because the player cant control units that easier). Adding AI to some missions, especially in enhanced mode would be great.
Well, i had to adjust it during testings. You might be just really good.

who knows?
The second thing i want to add - the only mission where you can choose faction is the last one, it is a little sad. Moreover, Alterac, Kul'Tirus, Gilneas are unplayable, although their forces participated in that campaign according to the lore.
What you mean is a little sad? It's a choice option in the end to try it with different techtrees at full capacity.
Alterac, Kul Tiras and Gilneas are unplayable because, as you say, their forces participated in that campaign according to the LORE, but not with actual forces in the Warcraft 2 game. Alterac was just standing back, as its contribution to the Alliance was minimal and its forces weak. Kul Tiras supplied ships and naval support(we only see it on the field during Beyond The Dark Portal). Gilneas fought in the battles of the first chapter and then went neutral real quick, or so i heard.
The story lore-wise changes a lot from Warcraft 2 times to Warcraft 3 times. i downloaded a book which narrates the events from a Warcraft 3 perspective and it syntetizes Warcraft 2 events much briefly compared to how they played. Like it depicted Perenolde to just have stood at Alterac's mountain pass waiting for Doomhammer to transit, telling him "hey don't attack my nation and i will grant you safe passage, k?" and that's it, while we all know that Perenolde had a major scheme and actions that influenced the events of the second war. However, Blizzard dug a lot of plot-holes in their warcraft stories anyway, so that's not big news.
For example, Lorderon Knight with 3 armour upgraids vs Stormgardian Knight with 3 attack upgraids - aren't their equals in combat?
But you are implying that they would fight against each other like they're the only 2 human subfactions, while there are others that would require different strategies according to the subfaction they'd face. A good example is Dalaran, whose magical arsenal requires you to use more brain than just muscle.
However full stack of Lorderon Paladins can wipe enemy base even easiar than full stack of inquisitors
You're obviously talking about late game factors here. Inquisitors can steal a large amount of health when fully upgraded AND Fiery Spirit researched. Their soft resistance makes them bad in defense, but at that point all you have to do is let them loose and attack.
Lordaeron, yeah, their Paladins are strong and even stronger with the Spiked Armors. I could have given them a Medium armor to compensate for the resistance, but then they would have been weaker defensively so i had no clue at that point how to really balance that, because medium armors take less damage from piercing attacks, and you already have Footmen with Defend, etc.
Appart from that, ships are not customised at all, although it would be great, especially introducing Kul'Tiras.
That's the point: Kul'Tiras is not introduced as a custom faction simply because it didn't show up in the original Warcraft 2 game. The campaign would have been even tighter showcasing more subfactions by then. Besides, as i said, they supplied ships, and that's the reason you see Destroyers icons as Green.
Artillary can also benefit from customisation (Lorderonian have to enroot to attack, Stormgargian has quick movement spead but cannot attack closer then 600 distance, Kul'Tiras has cannons (mightiest artillery in the game?)).
Of course, that's just my vision.
It's an interesing one and you'll see that i went for that option in the Orc campaign. I couldn't see how to custom Balistas in any way so i just left them like that. Besides, they are supplied by Kul Tiras, another faction which is not featured in the actual Warcraft 2 game. I wasn't even going to customize the Elven Archers in the first place, but had to do so when i realized the custom material was looking too poor. I had but much fun in exercising the many ideas i had during development, though. That i can tell.

Also, i need more custom models if i have to invent something for the custom Artillery units. I'm still in time to add further things on later updates. Never say never.