The first thing is to move away from the -Paper, Scissors, Rock- mentality of Total War; Spears beat cavalry, Cavalry beat Swordsmen, Swords beat Spears. The reason for this is twofold;
1) Sword units are not very historical, I'm not saying they didn't exist, but the vast majority of fighting was done with spears, even those unit that did have swords would have started with a spear to begin with and pulled out the sword if the spear broke or they wanted to throw it. The reason they were mentioned in historical texts is because they were the exception to the rule and it was assumed that everyone knew that they would have had a spear as well.
Swords certainly weren't (and still aren't) an anti-spear weapon. They also aren't great at getting through armour compared with a spear.
2) By removing the paper/scissors/rock mechanic of M2TW you force the player to use the other factors to win battle; terrain, morale, etc. In fact morale and strategy becomes the most important thing when you remove swordsmen from the equation. Outflanking the enemy becomes really important because you can no longer rely on throwing your heavy infantry at their spearmen.
I'm not saying there won't be infantry, there certainly will be and some will wield swords, however they will be rare and therefore serve a different purpose. Non-spear infantry will have mixed one handed weapons and shields or will be 2 handed weapons like pikes and bills. The mixed one handed weapons will include maces, single handed axes and swords. They will be good against spearmen (generally think of them as being more trained, non-levy troops) however the Levy Script will ensure that they are non common so you cannot spam that unit to take out the AIs spear heavy army.
My idea is that generally you would have spear infantry as standard (and a very large part of your feudal levies) and some other specialty troops depending on who you are and where you're mustering, plus the possibility of mercenaries.
If there is an "infantry killer" it should be the two handed troops (billmen, halberdiers etc.) which would have a very high attack but their lack of shield would be their weakness (vulnerable to archers). However these troops should also have the anti-cavalry trait as well.
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