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I'll share my IMHO:
Personally, I always choose skills based on a specific goal. For example, if I'm going to attack an opponent and have Berserk and Basic Fire in my arsenal, I'll focus on upgrading Fire, neglecting everything else.
In general:
1) Why would anyone refuse Logistics (almost never)?
2) Earth – for beginners, the Expert Earth skill significantly increases their attack power; for main heroes too, plus the hope for Teleport, Explosion, Resurrection, Animate Dead for Necromancers, Antimagic(!), and there are also some good spells.
3) Combat skills – attack, defense, no need to comment here; if the strategy relies on archers, then Archery too.
4) Wisdom – usually, but sometimes it's worth ignoring it.
5) Resistance – I almost never refuse it for the main hero.
6) Any other school of magic (depending on the situation); in general, I think Air is slightly more valuable for a fighter.
7) Pathfinding – depending on the situation.
8) Ballistics – only for a specific purpose (e.g., a rush on the 2nd level).
9) Artillery – if the attack is high, I often take it; on the 2nd or 3rd level, a ballista can quite replace a Titan:D
I think it's great to have one of the heroes with Scouting and Literacy.
Learning – I don't like it.
Navigation, Eagle Eye – useless. And Mysticism too (except for specialists).
Diplomacy – ban.
Leadership – a weak skill, except when you have to combine it with Necromancers.
Luck – a weak skill; it works when units have fixed damage or double attack (Necromancer Knights, Marksmen).
But if Luck is available to Storms or Dogs, then they deal half the maximum damage. So, I'd prefer any school of magic to them.
And Tactics is great, especially at the beginning of the game.
Intelligence – it can also be good, but usually I take it for something specific, for example, if I found a scroll of Explosion; or just counting on the fact that the amount of mana will decide the battle.
If a mage is being developed, then slightly different skills are suitable for him: Wisdom, schools of magic, Intelligence, Defense, sometimes Sorcery, and all other fighter skills. Ballistics is much more useful for a mage.