You know, if it's one character that really got screwed over by timing more than anyone (besides those from series with rotating casts), I honestly think it's Takamaru.
Back in the lead up to Smash 4 he was a very talked about character, and by far the fan favorite when it came to potential retro character options. Like if you wanna talk about characters popular during the Smash 4 era that still aren't in, Takamaru is right with Isaac at like the top of the list. And his prospects looked pretty good, too! Especially since even if his original game was Japan only, he still had international appearances with Samurai Warriors 3 and Nintendoland.
But then later on it's revealed that while Sakurai did consider Takamaru, he decided against him due to his original game's lack of an international appearance, and instead made him an Assist Trophy. The roster was decided in early 2012...only for an international release of The Mysterious Murasame Castle to happen anyway in 2014 for the 3DS.
And then to make matters worse, general skepticism due to his Assist Trophy status affected his ballot turnout, more than likely, as the idea that the ballot would be used for a sequel wasn't a common thing at this point. So when Ultimate's base game arrives and brings back all of the veterans, there's only so much room for newcomers...only six non-echo ones, in fact. And when the competition consists of Isabelle and Inkling (two of Nintendo's most prominent characters), Ridley and King K. Rool (two of the biggest requests), Simon Belmont (a brand new third party character), and Incineroar (the obligatory new Pokémon), there just wasn't enough room.
And the DLC comes out! ...But Nintendo seemingly prefers first party DLC newcomers to have some synergy with their current console offerings, and because The Mysterious Murasame Castle is a retro game for the Famicom, it didn't make the cut.
All in all, I honestly think that if the Murasame Castle 3DS port happened at least two years earlier for international audiences, Takamaru would have made the cut for Smash 4. It was just a case of truly awful timing. And...honestly? I think Takamaru, alongside Waluigi and Isaac, are definitely first party characters to keep an eye out for next time. Especially if it's a game that isn't focused on bringing everybody back, and as a result would have more room for additions of Takamaru's caliber.