Pongashi may be the missing link between Candypop buds and Pikmins.
An urban legend says Shigeru Miyamoto thought of the idea of Pikmin gameplay when he saw ants in a garden working together, but as far as I can see, we have no such a legend about where the unique design of the Pikmin creatures came from.
Here is my hypothesis. Have you ever seen this plastic bag? Probably not, unless you have lived in Japan. This is a bag of puffed rice, called pongashi. This may be one of the roots of the design of Pikmin.
As you can see, this bag most closely resembles a Pikmin seed popped out of an Onion or Candypop Bud (the color-changing flowers). More importantly, it also looks like a Pikpik carrot. Actually, on the bag you can see the word にんじん (carrot). You may remember a Pikpik carrot is a vegetable on Olimar's planet, and a red Pikmin he first meets looks like the carrot so much that he names the creature Pikmin.
You may think a bag in the shape of a carrot naturally looks like a kind of carrot (Pikpik carrot), and since Pikmin resemble Pikpik carrots, the bag incidentally looks like Pikmin. However, most important is the fact that in the Japanese version, a Candypop Bud is called pongashi-gusa (puffed rice plant), although it does not look similar to puffed rice or a bag thereof at all. But the flower is functionally similar to machines that make puffed rice, which pop out pongashi after rice is put in, just as the flower pops out Pikmin seeds after Pikmin are put in.
Therefore, I presume that the flower was named pongashi-gusa because it produces Pikmin, which look like a pongashi (bag). Pongashi was quite popular among kids decades ago; as many childhood experiences gave Miyamoto the seeds of video games, this bag might have given him the seed for the design of Pikmin.