I like most of the thoughts around this mod. It seems to me that the game could be significantly improved with more and better armors and weapons rebalanced. Mostly I think it should undo some of the stranger ideas that have crept into the core game design.
The weapons should be 'balanced' in the sense that they all have a place to counter certain other 'defences' (whether that be armor, mobility, monsters, etc).
What can't be easily changed of course is the basic combat mechanics around accuracy vs dodge, attack vs defence, hp, etc.
If they are to be tied to a tech tree, it seems to me that there were not that many different 'eras' to represent.
1. Early weapons prior to metal technology (clubs, spears, poles, etc)
2. Metal weapons (blades of all lengths, hammers and axes, etc)
3. Anti-armour weapons (hammers, polearms, maces, etc). These were brought in as a response to the heavier armors developed in Era 2.
The idea that long swords are better than short swords (for example) and that later weapons in the tech tree are better than earlier weapons in the tech tree is a flawed concept, and we should fix that. If anything, we could have better quality weapons later in the tech tree, but length of blade is a choice, and longer isn't necessarily better.
What I'd like to see happen with armour
No reason why we can't represent the main kinds of ancient armour. Loosely speaking, and divided into 'eras' (tech tree levels):
Heavy Plate (an early kind of plate, very heavy but crudely effective)
Laminar (such as Lorica Segmentata)
Splinted Mail (maybe)
Each has strengths and weaknesses, and their costs in weight, metal and so on means that the tech tree should be de-emphasised (but not gotten rid of entirely).
The trick here is (imho) that all weapons can kill a man, no matter what armor they are wearing, and we should be fundamentally rebalancing the armor so that all weapons are affected by all armours (more or less depending on their strengths), without the need to research 'killer' weapons at the end of the tech tree in order to affect an armoured man (for example).
What I'd like to see happen with weapons
Clubs and staves are fine early weapons but not that flash when armor kicks in. The first armies should be spear based, since that only requires wood and basic tools. The spear survived for millenia as a weapon type, and only went out of fashion a few hundred years after firearms were developed. Once you know how to make spears, you can make short spears, long spears, pikes (although only if you have the right trees). The real strength of spears is against mounted units, which they should have a bonus against (preferably getting their retaliation in first!).
Once metal weapons start, you get blades. In game, daggers, short swords, long swords, etc. The difference is in weight, speed and attack. I would be happy to see something like:
Weapon Attack Weight Initiative
Dagger 6 1 +6
Short 8 3 +3
Long 10 5 +0
(the numbers need trialling for balance, but you get the idea)
We can do some modelling to see the overall effectiveness of different weapons vs different armor combinations, in order that they all have an appropriate use.
I would like to see up to two retaliations for every weapon. That means to get a 'free hit' against a unit, you would need to be flanking or outnumbering them.
Bash and backswing are a bit silly, and can be removed. The main point is to have the right combination of cutting (the basic best weapons), piercing (spears and arrows) and blunt (specialist weapons for tackling heavy armour).
What I'd like to see happen to the tech tree
There are really only 3 or 4 basic developments in arms, and the same in armour. Levels beyond that could be introduced only to add 'masterwork' type bonuses, i.e. better quality weapons. My idea would be to allow a great range of weapons quite early, and I think that would be more fun and more 'realistic'.
Alright that is getting a bit long. The main point is I think your idea is well worth exploring and trialling, to try and bring additional balance (and fun!) to the game.