It didn’t sell that well but gained a bunch of fans and even warranted a sequel on that same console. I’d just contend that with two sequels Nintendo doesn’t know how to blow it open into a system seller, which is why they skipped the chance to put out new franchise content on the Wii (all we got were the ports) and were reluctant to make Pikmin 3 at all.
Ultimately, you have to think of the cost. Pikmin 3 cost much, much more to make than Pikmin 1 and 2. I bet it cost more than both of those games combined.