I am not sure if all these factors are actually relevant, but here we go:

• /gamerule mobGriefing false
• Hard difficulty
• Villagers inside a house
• Zombies trying to break in (difficulty is set to hard, so they would try to break the door, but /gamerule doesn't let them)

These things MIGHT be related to the issue. I get really bad delay on picking items, killing mobs and even brewing.

NOTE: this is on SINGLE PLAYER, clearly an internal server problem.
NOTE2: when I kill all the zombies, the delay is gone. There is probably something wrong with the new zombie system as well.