To be fair, a lot of people during Smash 4's speculation automatically ruled out the Wii U games getting many stages because development started long before the Wii U was even released. Despite that, we still got Mushroom Kingdom U, Gamer, Garden of Hope, Mario Circuit, and Wooly World.
It's highly unlikely, yes, but I don't think a character's chances are "shot" just because they debuted after development started. Even if Greninja/a Pokémon rep was planned from the beginning of Smash 4's development, Sakurai has shown us that he's more than capable of adding characters after development has started. He claims to be less stressed out over this game than he was with the previous entries, so if he thinks he has the time and resources available, I could see him adding someone like Spring Man later in development. Like you said, he'd have well over a year and a half to work on the character.
I don't remember people saying there wouldn't be Wii U stages, people were especially poorly grasped on developmental timelines and its implications back then (such as Tropical Freeze being used as reasoning for why Dixie Kong was a likely newcomer in Smash 4), but regardless a stage is a lot less developmentally-intensive than a playable character. And people got to stop bringing up Greninja as evidence for Arms/Xenoblade 2/etc. getting a playable character; first as stated by Sakurai himself
a placeholder for a future inclusion was an exception made just for Pokemon, conversely he stated Robin probably wouldn't have been in Smash 4 if Awakening released just
six months later (for reference Awakening released in Japan just a month before Smash 4's roster was decided). Additionally,
Greninja was still decided very early on before he was even revealed publicly (with Sakurai's only references for him being concept art
), Greninja was not made mid-development. Also from Sakurai's words, a new playable character
takes over a year to create, that is not something you can just squeeze into development right in the middle of it, a whole new unique character is not getting added mid-development that isn't a case as special as Brawl Sonic's, especially not in the age of DLC when you can just wait until DLC instead of delaying your game for a single character.
Whether it's deciding an inclusion for an Arms character back in December 2015 or deciding to add an Arms character mid-development, either scenario not occurring is about as certain as you can get for a character's exclusion that wasn't flatout disconfirmed. The only scenario an Arms character still makes it in is if Sakurai decided to make one a clone, which doesn't seem possible as no character on the roster is a good cloning base for them.