A new loadout system might not be difficult to implement, but since it would break Native compatibility it might be tough to get players. Hopefully since MP and SP launchers are separate MP mods could be downloaded directly through the server list... though I doubt that will be the case.
Probably making a client-side mod that adds equipment perks (like neoGK expanding equipment options) would be easy enough. But going back to a 3-class system with full loadout control would be a lot more work and would probably only appeal to warband players.
Captain and skirmish are the best modes for the new 6 class system tbh. The issues you mention could very easily be fixed server side by simple rebalancing; adjust armour/damage values, change relative sizes of groups, etc. Anything players have to manually download will reduce population to 1/10 native at best.