Thought we already had a mod suggestion thread somewhere around with plenty good suggestion in it. Guess it got buried.
But anyway, most if not all existing mods that change the troop trees and add new features in one way or another make the game harder, the logic being that Native is not difficult enough (which it really isn't unless you impose specific self-restrictions). However, there are a few that merely switches the difficulty curve, meaning it makes the early game harder but the endgame somewhat easier - Native Expansion (sans Dark Knight invasion) and Blood and Steel, for instance. PoP will make you sweat blood until you know what merc to recruit, at which point you'll have an army comprised of guys that make the mod's equivalent of Swadian Knights look like complete pansies.
Not sure if original mods count, but IIRC (I played that a long while ago and heard the mod's developed a lot since then) Solid and Shade for 1.011 will give you a much easier time even at the start given that you pick a very specific character creating option set. Also TLD, if you don't mind picking up a bow.