Game Freak is second-party but the Pokemon franchise is a massive cash cow for Nintendo. Of course, there are going to be playable Pokemon in Smash. Are there any other second-party series that are cash cows for Nintendo? Golden Sun, Sin & Punishment, Legendary Starfy, and Custom Robo come to mind but they aren't cash cows like Pokemon is.
Oh, and HAL Laboratory WAS second-party at the time Smash 64 was made. HAL Laboratory is responsible for Kirby and Mother games so of course Kirby and Ness got in Smash 64 then. Rare WAS second-party at the time Smash 64 and it was responsible for the Donkey Kong Country trilogy. But the Donkey Kong character himself is 100% owned by Nintendo so Donkey Kong got in Smash 64.
If HAL Laboratory (then a second-party) made Kirby and Mother games before they made Smash 64, then Sakurai (a then-employee of HAL Laboratory) was biased to add Kirby and Ness plus it was probably easier to get the rights to add Kirby and Ness in Smash 64 for the same reason it is easier to just add first-party characters. And now Sakurai runs his own company Project Sora and his company was responsible for Kid Icarus: Uprising, I can totally see Sakurai adding at least one (or better yet, two) new Kid Icarus character(s) in SSB4 even though the Kid Icarus IP is 100% owned by Nintendo.
Characters from first-party Nintendo games tend to have priority over characters from second-party Nintendo games. As a general rule of thumb, I just look at who developed the game instead of looking at who owns the IP. If I see a game that is said to be owned by Nintendo, great, but that doesn't mean the character is likely to get in Smash unless I know which development team developed the game. Grade-A choices are probably from post-Brawl games developed by Nintendo EAD, Intelligent Systems, Retro Studios, Monolith Soft, HAL Laboratory, and of course Project Sora. It also helps if Shigeru Miyamoto worked on the games regardless of being a first- or second-party.
Nintendo EAD: Toad, Bowser Jr., Mii, Zelda characters, Animal Crossing characters, Balloon Fighter and Takamaru (Nintendo Land), Pikmin characters
Intelligent Systems: Paper Mario, Mallo (Pushmo), Chrom, other Fire Emblem characters
Monolith Soft: Shulk
HAL Laboratory: Waddle Dee
Project Sora: Palutena, Medusa, Magnus, other Kid Icarus characters
Nintendo SPD: Ridley (Metroid: Other M), Little Mac (Punch-Out!! Wii)
What about retro characters? It's usually the ones from Nintendo R&D1. It was responsible for Ice Climber, Kid Icarus, R.O.B. games (Gyromite and Stack Up), and the entire Game & Watch line. It's also responsible for NES classics such as Balloon Fight, Clu Clu Land, Excitebike, Urban Champion (the same characters rejected by Sakurai before selecting Ice Climbers) and of course Duck Hunt
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