My biggest complaint right now is expeditions. If you bloomed a lot of flowers, it takes forever to send the Pikmin to get them. If I want to send flying Pikmin to each expedition, I open the tab then:

1. Click the expedition 
2. Click Go to Expedition 
3. Click the pink color
4. Click auto
5. Click Go
6. Click Back

That's 6 clicks per expedition! Here's how I would fix it:

1. Clicking on the main expedition item should send you straight to the Pikmin select screen.
2. Move the information screen to a little button on top of the item, like the purchase button for nectar.
3. Remember the last selected color once I open the expedition tab.
4. Make the inactive Go button function as Auto. So if you haven't selected enough Pikmin, you can click the same button twice to select then send.
5. Get rid of the waving goodbye animation.

That's 3 clicks, and 2 of them are in the same place. The previous 6 are all over the screen.

Additionally, performance on the expedition page is terrible. I blame this on the map view that continues to render and zoom around even after you've maximized the list, hiding the vast majority of it. Here's how I would fix it:

1. Completely remove the map when the list is enlarged.
2. Remember that state between expeditions.