[1] because new game+ would make you have to play through the entire game again. this way you can go back, get everything, beat the boss for 100%. the game is made to be replayable anyway. you'd gain nothing from NG+-
[2] Piklopedia has been replaced by the Fruit descriptions you can find in the notes section.
[3] because they don't make sense there. Whites and Purples are entirely useless for Pikmin 3's design. this has been discussed to death already but here's a summary: 7 types are overwhelming and confusing; both of them have no design justification for this management-focused game whereas they did have relevance in the combat-focused Pikmin 2, their abilities were partially moved to other Pikmin, they didn't have Onions, they actually do serve a purpose in mission mode where it's all about speed and high scores and you get predetermined Pikmin.
For 1, I actually phrased that really badly for some reason. I meant post-game, not new game+. It's not really a huge difference, but I really liked the way Pikmin 2 pulled the "you beat the game, now complete it!" thing. I'm sure there's not much in the way of actual difference between that and the way the game plays now, but for some reason I'd really prefer a little cutscene to set up the rest of the fruit collection or some final task that takes place after the credits roll.
As for 2, I can accept the fruit descriptions as acceptable substitutes for the treasure reports (though I admittedly still need to actually look at that stuff. I usually like to fill in these sorts of things and then binge read. Also, I really wish they wouldn't have used repeat fruits. There's definitely enough types of fruit in the world that they didn't have to, even if they would've had to use some "obscure" fruits.) And the data logs are kind of neat too. But the lack of a proper enemy encyclopedia where you can mess with the enemies is really sad, and then there's the fact that Pikmin 2 had the full on descriptions from Olimar, Louie, and the ship. Just feels like a step down, which is a shame as that was one of my favorite parts of 2.
And for 3... I guess that makes sense, but I think I just mainly wanted them to use that chance to finally give whites and purples their own Onions and make them "proper" Pikmin types. By not even giving them a place in the story, they feel even further removed from the other types, which is a little sad.
Still, I did have a lot of fun with the game, and I'm definitely prepared to dig in more. I love the fruit idea, even if I was almost never in danger (outside of Louie reprising his role as a super big dick). And the bosses are amazing. My jaw dropped a little at the one in the swamp, just super cool.