I think a good compromise a longer form game could try is having no overarching time limit but setting it up sort of like Persona where you have X days to complete this story objective. If the time limits are short enough the deadlines would also actually have more practical threat than any of the previous games.
There are tiny hints of this in the other games, but you could do a lot more with the day system in general than just having one big deadline. That idea has never worked super well in practice because while Pikmin can be a short run, the players it will actually force to restart are also the ones who will have invested the most time into their playthrough. The game can be completed in under an hour, but it takes 6 and a half hours to fail at Pikmin. The idea of a Nintendo game of all things that can let you play for 6 and a half hours before making you restart from scratch due to a game over is ridiculously ballsy. The reason this sort of design still works for games that can be spoken of in "runs" is that said experience is usually a time investment of under an hour, not multiple days of play sessions. Adding the ability to restart from any day and the sliding deadline of 3 feel like acknowledgements that it's better as a threat than it is as a real thing that can actually happen to you.