NargottIt is very weak bonus, equal to +2.5-5-7.5% to melee offence, because only 25% of melee damage is retaliation damage.
You can verify this claim by looking at recordings of any fights and comparing the resulting retaliation damage, and the total melee damage.

You are correct. Skill itself is weaker to compensate for the advantage of the perks it offers - Chain Attack, Martial Arts (critical strike), Avenging Strike and Stun. Which are favoured among Might hero players.

Nargott 1) 3-6-9% ini boost is equal to 1-2-3 morale, but this effect consists of 2 components: first turn, and later turns. Standard leadership doesn't boost first turn of units, but necro leadership boosts. It means that with this skill, the undead will be ahead of the living on the first turn but slower in later fight.

Indeed. Generally Necro are on the lower initiative spectrum so it is a big effect. 

Nargott2) ideally, basic HP should also scale with hero level - but I understand that this place must be additionally searched in the exe file

Agreed. Though as a "feature" now the HP multiplier is made higher to compensate which is one more reason for a player to get War Machines if he wants to invest in them.

NargottSurprising change as your mod is heading towards weaker stats and perks, while the 4% retribution is an extremely powerful perk even by the standards of the original, up to +20% non-retaliation melee and ranged damage, that's more than many expert skills for 3 levels.
This perk at 4% per morale has value of 3-5 of original stats (5%).

Yes that was a mistake that will be reverted in the next release.

NargottIt's very good that you make logistics more combat skill. But extra forces is a rather boring bonus that does not affect the course of the battle in any way.
In my opinion, there is a more interesting alternative for logistics - this is a bonus to the starting ATB of units (5-10-15%, for example).
Moreover, you have already partially gone in this direction, increasing the initiative of the troops (undead) for leadership.
Necro leadership I offer a little differently: +5-10-15% bonus to initiative, but -5-10-15% penalty to the starting ATB of troops. In this form, this skill will be as close as possible to the natural morale, as it will not allow undead units to accelerate the onset of the first move.

Starting ATB is hard to modify (currently impossible). Due to the slower pace of MMH55, it is observed that players aim for survivability and/or hoarding of units in order to maintain pace throughout the game. Thus Logistics is one of a few new ways a player can replenish his stack count. Also Logistics had to be nerfed as PvP players all agreed that it provide extreme advantage  so we followed up with the movement changes to tone down difference between hero with and hero without the skill.