To answer your questions:
1. Sakurai wanted to incorporate a unique gimmick with Zelda/Sheik by making a transforming character with two distinct styles. It had nothing to do with relevance.
Besides, if relevance meant anything, only Young Link would have been in Melee, replacing the irrelevant adult Link.
You know why? Because Majora's Mask was the most recent "main" title in the series, not Ocarina of Time.
2. No, Ness would have been replaced. However, that didn't happen. Even in Brawl, we have both. What exactly are you trying to accomplish here?
Furthermore, Leif was the most recent main character in Fire Emblem. Marth got in before him. (Don't even DARE to bring up Roy. He and the rest of the clones were afterthought characters not in the initial lineup. Aside from that, he didn't even exist yet.)
3. Probably because Delphino is iconic and was interesting to Sakurai? Did THAT thought occur to you?
And while we're on the subject of stages, explain how we got a Kirby stage from Super Star (don't use the handheld bull**** here; Kirby LIVES within handhelds) instead of one from Squeak Squad, a Metroid stage from Super Metroid and one from Metroid Prime instead of a stage from Prime 2?
They sure as Hell were not relevant.
4. And yes, Lucario would have still been in Brawl. He:
-Was the most requested Pokemon character in Japan AND America.
-Is very iconic, which is rather rare for newer Pokemon. (None of the 3rd Gen were at his level.)
-Featured a potential unique attribute with his Aura capability.
Likewise, the 2nd Generation was the latest Generation in Brawl, yet only got a character as a last minute clone.
While Mewtwo was the most requested Pokemon for Melee, and sure enough, he got in.
Just like how now, Mewtwo is one of the most requested characters in general, and after him in terms of Pokemon is Zoroark. Both are more likely to be added than a 6th Gen at this point (unless one is revealed soon that somehow manages to attain Lucario level of popularity and iconicness in a VERY short amount of time).
Seriously, if you're going to make a case, MAKE SURE THERE AREN'T GLARING COUNTERPOINTS.
As for your "subconcious" theory, unless you're in an advanced field of psychology, don't be spouting this kind of crap as if you knew what you were talking about.
If Sakurai changes F.L.U.D.D., it will be because he finds it doesn't suit Mario's playstyle, not because it is irrelevant.
Aside from that, all of this is COMPLETELY OFF-TOPIC to Dr. Mario.
So I suggest you quit the argument while you are behind.