Great ideas that won't be included unless there is a direct benefit in doing so...
I think the pit-jump would be be a useful addition. It could help DK go out just a bit farther when edgeguarding, allowing him to better capitalize on his formidable horizontal recovery. It could even allow the roll itself to be used for edgeguarding.
Diddy could also be given this ability, so the work of programming it would have double the yield.
It's called development priorities. We could spend hundreds of man hours coming up with and implementing the dozens of ideas that sound really cool on paper but utterly screw with the game in ways we don't intend, or we could approach things a bit more realistically.
As for Link's Hidden Skills, they probably wouldn't mess with the game too much if just used a standard A attacks (or as dodges for his backflip, roll, and sidestep; or change his idle animation while holding item (you know what I mean)), and wouldn't even necessarily require attributes new attributes. Heck, they added an upgrade to the jump attack that has two hits, perfect for his f-smash!
But, animation takes work, and it's probably better left to someone more specialized in it, so as not to waste you guys' programming expertise.
I'm not a fan of making the Dees disappear on the ground. That removes something that makes the attack unique, moving more making it more like just another laser. If anything, they should stick around longer.
Rather than having Dedede control them, just make them smarter with their attacks. If the King has to take time out to give a command, a can't very well use them as a distraction.
A possible change for the move could be to make it so that Dedede can just drop a Waddle in front of him, with less lag than actually throwing them. This would make them better at blocking attacks against their master, and would make positioning them as obstacles onstage easier. It could be triggered by tapping, rather than holding, B, or by shield/jump canceling the move.
Other changes: remove the Dees' random tripping/stupidity, remove Dedede's throwing of items (to make the item settings less picky), and remove throwing nearby minions with A.
One thing his down-B needs is a quicker uncharged hit. It could also be given a horizontal boost, a la Minus, but, as others have mentioned, he doesn't really need more recovery, not to mention the counter-intuitiveness of pressing down to go sideways.
Neutral-B could give spat opponents knockback and damage upon striking someone, making it a useful move on teams. You could also make the spitting distance scale with damage, though that might be OP.