These concerns are all legitimate, but with a little tweaking I don’t think they have to be as significant as you make them out to be. Having stun unaffected directly by armor would be fine for me; and the change to stun chance could be a spread calculated as a percentage of remaining stamina rather than directly related to the stamina number (say -10% at full fatigue, to +20% at 0 fatigue for a maximum 30% spread), so more stamina would still be better, but it would be a much less significant difference, and armor would actually increase your stun chance slightly.
There are also some different ideas for how stunning should work that have been talked about in other threads, including switching it to AP damage. These could give more granular control over how debilitating a stun is, possibly with different levels of stunning depending on the force of the blow. I’d be interested in whether there was a way of making stuns affect your initiative, and if it lowered your initiative enough, you would be dropped off of the turn order into the next one. This would make initiative more important in determining whether a stun was effective or not, but I’m not sure if there’s a way to make that work without creating a lot of initiative exceptions for stunned units.
Stunning is obviously irritating when it happens to your brothers, and overall slows battles down a bit, but currently it is only really a factor when facing orcs. It is one of the things that most quickly feels ‘unfair’ for new players if they don’t understand it. I would want it to remain fairly rare, but occurring in a wider variety of circumstances.