I'd really like to have encounters become more difficult as your PCs gain in power. I enjoyed KotC most at the beginning, when every non-wandering-monster encounter had a significant chance of wiping me out. When I got to the slaver city (Taneriz?), though, I got obsessed with wiping out every last slaver instead of triggering the collapse of the city. As a result, I wound up with enough XP and gear to make subsequent encounters (like the fire giant citadel) a pushover, which made it a lot less fun for me. To be sure, this was my own fault and I've already started a new party that I'll consciously try not to let get too tough - but I think it'd be great to have the level of encounters scale up to keep you on the knife-edge of deadliness that KotC does so well.
I'm not sure the 3.5 D&D rules for ECL and scaling encounters are in the SRD, but the simplest way to do this would be to give the monsters extra HD or class levels in order to match the party's total ECL. Better still would be to also factor in the value of the gear the PCs are carrying, compare it against the expected value, and also magnify the threat if they're over-equipped. It ought to be possible to do this mathematically - i.e., to multiply each monster type's BAB, damage, saving throws, etc. by some percentage that roughly equates to what they'd get from added class levels.
A related thing I'd like to see is a change to the campfire system. Again, the most fun moments for me were when I didn't know when I'd be able to rest again - in situations where I could hit an encounter, go back and rest, and then hit the next one, I was torn between the desire to do so and the knowledge that I'd have more fun if I pushed it. Since this sets up an conflict in me as a player, I'd much rather have the game control the tension by limiting how often I can rest.
What if KotC 2 broke from the D&D paradigm of daily rests to recharge spells, hit points, etc., and instead said that you get these back by overcoming challenges? For example, maybe you get a "rest" when you earn enough experience to get a quarter or a third of the way to next level. Or (to avoid things like crafting items making it harder for you to rest, or scumming random encounters so you could rest) you could script a number of "achievement points" into each encounter, and when you earned enough you'd get spells and HP back. I think the d20 tabletop RPG FantasyCraft uses a similar system, and in my mind it's an elegant solution to something that's a problem in many editions of D&D and that gets worse in a cRPG version.