More interesting and varied combat. I absolutely love the idea of a monster that you absolutely have to use multiple Pikmin types to kill. Don't make it essential, so you weirdos can still do your single Pikmin type runs. An example would be a monster that is impervious to all attacks unless its shell is broken by Rock Pikmin, and then it has a watery body underneath that has to be tackled with blues. I don't know, just something that isn't touched on much in Pikmin 1 and 2 that I think would be interesting.
Also, weather sounds right interesting. Rain could weaken all Pikmin except blue. It'd be nice having to adapt to what is happening in the world. It would make it seem less like everything is just waiting around for you to do something too it.
Ooh! More monsters battling it out while you're not doing anything. I'd love to see a Bulborb go crazy on a Flint Beetle.
EDIT: Just thought of another thing - night sections. Maybe you crash land again, or for some reason your ship can't land so you can't get to safety. You have to make it to a certain area (a safe place to land, I guess) or simply survive the night while there are way more monsters, all of which are awake and actively pursuing you. You could decide which you'd rather do, simply run the entire time, amassing a veritable army chasing you, or you could decide to camp down with 100 reds, and fight the night away.
It would be very different to the quite relaxed nature of the daytime sections and I reckon it could be quite interesting.
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