The whole "epic quest to save the world" was pretty good, and the goodbye scene was good...but it lowers the stakes so much. In the Tokyo arc, their city, their friends and their family are at risk from Myotismon, and he even kidnaps everyone. There's dramatic tension.
Then they go back to the Digital World, where nothing matters. Hell, each time they kill one of the whatists, and entire biome offs itself.
Also, a lot of weird shit suddenly started happening. Kari is messiah? Shoot Tai and Matt for power-up? What the fuck?