We don't know if Lucas was planned for that reason either, however, if the rumor that Lucas was planned for SSB, this may be true. However, Ness and Lucas have similar moves in their games so that may have been part of the reasoning.
Unless Sakurai had a special preview to the story of Mother 3, and loved it so much that he had to put Lucas in, I'm pretty sure his pottential inclusion in Melee would have been soley because he was topical, because unless Sakurai somehoe had access to the unreleased 64 game, there's no way he could have really judged the character as worthey/not many fans would actually be asking for him to get in.
I remember reading somewhere that Link and Zelda are supposed to be culminations of all the Links and Zeldas (minus Toon Link and Zelda) that preceded them. Toon Link, however, qualifies as topical to an extent, but I don't see this guy going anywhere.
I wouldn't really see how exactly they are supposed to be culminations of all the other Links and Zeldas designed for Smash, since they were clearly taken straight from TP. Now if you were to argue that TP's versions of them were supposed to be culminations, then that's another thing, but I kind of doubt that, seeing as their adult versions were only really used in OoT and TP, rather than the other games.
And I don't think Toon Link is going anywhere either, since he's technically still topical, given PH and ST. In fact, out of all of Link's incarnations, that one is the one that's used the most at this point.
As for Pokemon and Fire Emblem, I think this is an interesting area. People can see other reasons why Ike was included (popularity, being the first 3D lord, and the second lord to have more than one game), and Roy was planned for Brawl. Pokemon seems to get its various gens through the Pokeballs and the playable ones are up to popularity.
Roy actually reinforces the idea that at least FE is governed by being topical, since his game wasn't even released in Japan when Melee came out. Also note that pretty much all of the Pokemon from Gen 1 and 2 were just taken from the last Smash games. (Bar Meowth kind of, since he worked differently there)