The caves and randomized layouts of most of them are some of my favorite aspects about 2, but it's a significant gameplay change from the first game, so I can get why they're not for everyone.
I don't really see how most of them are "ugly", though. Only some of the early ones are really bland looking, and even then almost all of them have unique features, designs and plants to help them stand out or add to the immersion.
Having said all that, ,however, I do agree 2 seriously underutilized the potential of having two playable Captains. 3 handles having multiple Captains much better, both by having a new type of time limit and by adding several new mechanics that allow the Captains to cooperate and directly help each other, in addition to still being able to manage separate Pikmin squads on opposite sides of the map.