Other than the lackluster "gun missions" at the beginning (hampered by bad gun-play on anything but "easy" difficulty) I really enjoyed the single player campaign in JK2. I thought JKA's was more fun, and ultimately JK/MotS felt more groundbreaking (especially JK1), but still great overall. (and JK1/MotS are still supported via places like JKhub.net and Massassi.net)
I lost interest in JK2 multiplayer mainly because it seemed like it was ONLY 1 on 1 duels that people were playing (if they were even playing and not role playing). JKA was more fun for me online, though a couple of things in JK2 felt a little better (like CTF). I still run my dedicated server for JKA. Can't help you with JK2 though.