Maybe it's because Golden Sun was on the GBA while Pikmin was on the Gamecube. Pikmin 1 and 2 most likely sold more copies than Golden Sun 1 and 2. I think it made Olimar more "worthy" of an addition when compared to Isaac.
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Plus Isaac is yet another generic RPG-swordkid. Olimar is quirky and recognizable to anyone who played Gamecube.
I don't quite get it, Smash Bros on N64 was very much All-Stars. Mario, Luigi, DK, Link, Fox, Samus, Kirby, Yoshi, C. Falcon, Pikachu are the heaviest characters from most important Nintendo games. Earthbound and Ness are quite known and unique too especially back then and Jigglypuff is, well, is.
Melee mostly added extra important characters: Bowser, Peach, Zelda, Falco, Mewtwo from the same series, some as clones. If I remember only Ice Climbers and Fire Emblem were new entries, arguably the next biggest series with potential characters. Oh and Game & Watch as blast from the past.
Brawl continued giving important sidekicks/villains: Diddy Kong, Wolf, Dedede, MK, Lucas, Lucario, Fire Emblem got new characters. New entries from currently (well post-Melee) hot stuff: Wario, Kid Icarus, Pikmin. Introduction of 3rd party characters and R.O.B as "new" Game & Watch.
So logically I would expect SSB4 to have: More important allies/villains of majors and emphasis on them (King. K. Rool, Ridley, Toad, Krystal/Slippy Toad, Meowth, Dixie Kong, Samurai Gorah, Waluigi, Palutena). 2-3 new series entries with emphasis on newer ones (Xenoblade, Prof. Layton, Paper Mario. Perhaps Punch-Out! which is also on Wii). I could see Duck Hunt Dog being the follower of R.O.B as a quirky blast from the past and a representative of Zapper. 3rd party characters are new and unknown so I wouldn't be particularly surprised if they were both changed or removed with no replacements, but I guess there will be 2 new ones at tops (licensing makes guessing tough, but I guess the pool is Megaman, Pacman, Hayabusa, Belmont, Ryu, Bill/Lance and Bomberman)