While I wouldn't label JK2 as the best ever, it is in my top 3 list.
I would still list Half-Life as my #1. Not only did this game challenge you, but it revolutionized the FPS shooter at a time when they were both in their prime and needed innovation beyond the standard "shoot this person, jump, get rocket launcher" era.
What really makes HL the total package is the mulitplayer. I for one, wasn't impressed with JK2 MP outside the saber dueling modes. It just seemed like the same ole Quake style DM I have been experiencing in every single game since well.. Quake.