I feel like it’s a lot like the weapon breaking in Breath of the Wild - one of those systems that imposes heavy limits on players to enforce their creativity and flexibility in their approach.
I know a lot of people approach every game in a completionist, meticulous way where they do every quest, never use any consumable items, etc; and it often ruins the fun. It’s also why Ubisoft had the somewhat crazy idea in Far Cry 5 of actually forcing you to do story missions after game progress, trying to use designer mechanics to push some variety into people’s game sessions.
In Pikmin’s case, and I think Dead Rising / Persona too, the time limit is meant to get you to prioritize path planning so you get as much as you can done in a certain span. The core gameplay of Pikmin just isn’t all that interactive when you have all the time in the world for it - it’s built around the benefits of delegation and synchronization.