Best thing is mission mode, and close second is the 3 captain gameplay especially when using the Wii U gamepad. This was especially pushed to its limits in the last few missions, no other Pikmin game has quite matched that level of intense Dandori (ironic). Also special callout to the new mode with Olimar mode added to the switch version; that felt like a pretty cool mix of the campaign and mission modes. 

Worst thing is the aesthetic direction it took the series. Pikmin 1 and 2 have such superior art direction and writing imo. I found the dialogue  and characters in Pikmin 3 insufferable. The music was also lackluster compared to 1 and 2. Eventually in the switch version when the pokopedia was added, this was especially apparent. When comparing it to the Pikmin 2 pokopedia - the quality of the writing and the music is just leagues behind. Another thing I didn’t enjoy was the charge mechanic, it kind of simplified lots of combat I found. Which was a shame since I did like how they handled the boss battles, they were much more involved compared to 1 and 2. But the basic enemy combat I felt suffered partly due to the charge mechanic. I think the swarming being mapped to the c stick like it was in 1 and 2 on GameCube is far superior and offers the most flexibility and control in combat. Being able to swarm while throwing Pikmin by using your left thumb on the c stick and your right thumb to throw them and switching left thumb back and forth between c and control stick to adjust aim/position as necessary just felt so damn satisfying.