If you don't think Cities and Knights is complicated enough as it stands, here are a few extra alternate rules you can add. Thanks again to everyone who emailed me these!
Quicker games - Cities and Knights can be a lot longer to play than normal Settlers. One way to speed things up is to start everyone off with the first city improvement in every category already done. Also, you can ignore the event die whenever the barbarian ship is rolled for the first round or two of play. This takes away the early excitement of defending against a quick barbarian attack, but allows everyone to build up a bit in security to start.
Protect the Weak - This variant for Cities and Knights makes it easier to win for people who like to focus on expansion and leave few knights to protect themselves from losing a city. Whenever the barbarians attack, you only deactivate a number of knights equal to the number of cities instead of all of the knights. Also, you have the players with the most active knights deactivate theirs first, so that the players who contributed the least are usually left with theirs active (if they were active to being with). In case of a tie for who should deactivate the last knight, the player with more victory points always deactivates first.
Expansion For the Win - This variant for Seafarers of Catan encourages more expansion into remote islands. When a player places a starting settlement on a coast they immediately receive a ship and a road to place instead of one or the other. Also, whenever a player creates a settlement on a new island for the first time they get an extra half a Victory Point, instead of just getting one extra VP for the first island they expand to.
Robin Hood - This variant is meant for Seafarers of Catan, but can also be used in Settlers of Catan. Whenever you place the robber or pirate you get to steal one resource from all players with an adjacent settlement/ship, instead of just one. This way the robber always acts as if the Bishop progress card in Cities and Knights had been played.
Speed Game - This variant should only be used when all players have a firm understanding of the game. When playing this way, all players may trade and/or build at any time. However, they still may only play development cards on their own turn. This makes the game feel a lot more like Pit or Dutch Blitz and can be a lot of fun.