I think I kept track of at least the next 3-4 pikmin in my line and used smashes/aerials/rosa parks more than whistle to organize them.
You can easily check to see what you have while you're running, jumping, falling, or just moving in any way.
For grounded organization, you can easily use Usmash to cycle through one or Dsmash to cycle through two.
Sometimes I'd shorthop FF Uair/Fair to cycle one while checking the rest of my line, if I had space to do so.
You can toss any unneeded pikmin over the edge. If they're white, you can just toss them at the opponent. They have like... 4 HP, so they die when an opponent so much as gives them a mean look.
If you're airborne (like if you're recovering and want to get to a purple or something), you can Uair to quickly cycle through without tossing them away.
I don't really like whistle to sort. Keeping track of whistle colors is a bit of a hassle when you use it a lot for super armoring through things, and I didn't like the chance of accidentally FFing when using it in the air. That's just me, though.