I just like the fact that he's smiling
I don't know Sakurai--I admit that. But I want to speculate anyway. Seeing as Roy had to be recreated from scratch, Pichu and Young Link would also require more work. I think Roy had more popularity than either of the two and thus, Sakurai created him. Also Pichu has a different model than Pikachu (I believe). However, I'm told that Pichu is quite popular in Japan--so he could return, I suppose. Personally, while Toon Link and Young Link are different characters, their relationship to Link is the same "Younger, more nimble" link. A problem with Young Link is that he has no unique characteristics to merit being put in as a third Link. Wolf has a more aggressive non-laser based Gameplay compared to Fox and Falco--Roy is slower (I could be wrong on that), has a Fire effect and has the base-sword style of gameplay compared to the moderate shorter Lucina and the faster tip user, Marth. "But what if Young Link got a complete overhaul?" We haven't exactly seen that with anyone. Only thing I can see is him returning due to the 3D N64 remakes but even then, it's kinda a stretch. Also, I want to say that those two are from Melee and aren't Melee-Brawl veterans like Ice Climbers (though, nor is Snake which I guess goes against my point XD)
Now, Squirtle and Ivysaur, I am less sure of. The transformation gimmick being "cut" for Super Smash Bros 4. While this isn't a direct shoot-down like the Ice Climbers, one would assume Sakurai thought Charizard was the superior of the three. In my opinion, there are 2 things that could've happened. One, they were only interesting as part of the transformation gimmick and two, the developers couldn't find a way to make them adapt on their own. Or maybe when the Pokémon Trainer died, he only had Charizard out and the other two are now forever trapped in their balls--muhuhahahahaha.
EDIT: also, I figured to the common gamer, the absence of Snake in Smash 4 would hit more than the other 4 you mentioned