Hey Sawesawe, thanks for the questions (which also acts as a bit of feedback for me to see where things could be explained more clearly).
Trait skills are my take on the equivalent of classic D&D attributes (Agility = Dexterity, Command = Charisma, Fortitude = Constitution, Strength = Strength (obviously) although I have used Magic, Senses and Will aswell. Command is probably most used when interacting with NPCs or intelligent monsters or for recruiting followers.
The only restriction on weapons/armour is that if someone is wearing heavy armour (i.e. chain or plate) then athletics, agility (i.e. sneaking) and magic using checks are at disadvantage due to the bulk/weight of the armour. One of my design goals was to get rid of some of the classic limitations (i.e. a wizard can't wield a sword or use armour). In HoA a Mage could wear leather armour without penalty but if they wanted to wear heavy armour then they may be less effective at using magic. Essentially I am trying to give the players some choice and some benefits/constraints rather than saying "no you can't do that". If you want to play Gandalf wielding a longsword then go ahead.
Good spot on the weapon feature stun. The intention was to stun something on a critical (human sized creatures or below) hit and this was written before I made a tweak to the combat manoeuvre rules (see below - when you can now perform a manoeuvre automatically on a critical). I need to think about this but tempted to just change all weapons with the 'stun' condition to the 'bash' condition (i.e. if attack misses by 1 you do half damage). This creates a nice choice over use of bladed vs. impact weapons.
Combat manoeuvres were changed later in development as my players didn't really engage with them at first. Currently you can try a combat manoeuvre or one will automatically take place on a critical hit. I would absolutely encourage use of other skills (like strength or agility or even athletics instead of melee attack) if the player makes a case for it.
Example: If Thrudd the Barbarian wants to grapple Lurko the Thief to stop him getting away. I would allow him to use melee skill or strength skill vs an opposed strength (to push him off) or agility (to dodge/avoid) the grapple.
When learning new skills you can choose to learn any new skill or level up an existing one. Potentially if you focussed all your skill increases in one or two skills you could reach the max d12 by levels 4-5 and it plateaus at this point and thats fine as I wanted a lower powered game where people can max out their skills. Hopefully adventures will throw a variety of challenges at players as opposed to just combat such as tense negotiations, traps or puzzles so people maxing our melee or ranged combat is not an issue (and the fact that a base roll of d20 vs a maxed our roll of d20 + d12 means there's plenty of 'swing')
Hopefully, I've clarified your questions and this is all great feedback so thanks for taking the time to post.
I hope you enjoy the game.