For the past two Pikmin games, the Pikmin have unquestioningly served Olimar and other captains, never flinching in the face of danger and often flinging themselves towards certain doom. There is a simple devotion and dependency here that was eventually translated into
famous Pikmin "Ai no Uta", or Love Song. Indeed, who here can forget the subtle emotional bond observable when Olimar first escaped the Pikmin Planet?
I've played both Pikmin games extensively, but losing Pikmin has never been easy, even when you could freely replenish your Pikmin numbers by revisiting the onions. For me, the feeling of loss when a single Pikmin died was a strong emotional discouragement against feckless tactics and bad decisions.
Looking at the ideas in this thread has raised in me the notion that a lot of what other people see in the Pikmin games are the themes of conquest, expansion, and exploitation.
Do you remember how in Pikmin 2, Olimar's company sent him back to the Pikmin Planet to essentially exploit and harvest its resources? Imagine that this becomes the norm: Pikmin are being domesticated and used as slave labor, paving the way for large companies to plunder the Pikmin Planet for treasure, leading to unchecked prospecting and the eventual establishment of colonies. Pikmin themselves are being altered for use by the companies: genetically modified Onions produce purple and white Pikmin, for example.
Olimar is recruited into one of these colonization efforts, and the first part of the game deals with him using Pikmin as part of the mining efforts: gathering treasure, clearing out wildlife, and such. Some of the puzzles here would involve using Pikmin to gather parts and assemble machines, and learning to use the new features and gadgets employed by companies to "farm" and organize Pikmin.
Eventually, the Pikmin are recruited to help assemble what amounts to the atomic bomb: a terraforming device. To further the expansion taking place on the Pikmin Planet, it is essential that its environment be made non-toxic to Olimar's people, even if doing so would wipe out life on the planet. Faced with the unblinking beady little eyes of Pikmin he has raised from pellet to full bloom, Olimar turns against the companies, swearing to undo the damage they are causing before it goes too far.
In this frantic second half of the game, the puzzles and exploration from the first game are now joined with the combat and tactics of the second as the player works to reverse-engineer and disable the colonies and their machines. Olimar will still have the new tools to control the Pikmin; they will simply be more difficult to use or replace. Pikmin armies controlled by the colony would also reintroduce the PvP aspects that were touched upon in Pikmin 2; this could help players prime themselves for online combat, as well. Olimar will have the opportunity to liberate enslaved Pikmin Onions, bolstering his own army or adding special varieties that were bred or genetically altered by the companies (some of which he had worked with while employed).
So the Pikmin story comes full circle: Olimar ultimately owes his life to the Pikmin, and they in turn need his guidance to escape certain doom.
But that's just an idea I had.