Just because he doesn't show up in crossovers doesn't mean he's not important.
With that logic, the Bowser Jr. and the Koopalings didn't matter until the mid-2010s since that's when they were brought to Smash, despite Junior having been a consistent major antagonist since Sunshine and Koopalings being frequent sub-bosses if you forget the hiatus between Superstar Saga and New Soup Wii.
If crossover appearances really matter
that much to you though... Amaterasu's DLC costume in Marvel 3 is a Jon Talbain reference.
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So it's not like he never mattered.
Correct me if i'm wrong, but Bowser Jr never had a period of just being not being used contrary to Jon since his debut. Like he was the main big bad of Sunshine, which came in 2002, and after it, he became a recurring playable character in various spin-off games & a more or less important bad guy depending of the games.
Plus, ya know, Mario isn't a dormant franchise without any new game beside ports of the same 3 games for how know many years. Darkstalkers is a pretty niche series, so any appareance it's character get in official product matter much more than Bowser.Jr or the Koopaling appareing in any games those day. (for The Koopaling, there was a time, where they weren't used and it was indeed pretty long, but they more then make up that lost time now those days & were making a comeback thanks to NSBWii like you mentionned. Plus they were in alot of shows & spin-off back in the 80'-90', before suddenly dropping out of the map of the Earth. Due to how small Darkstalkers was & still is tho, Jon didn't have the same spotlight back in the day)
Also, take that what you will, but Bowser Jr & the Koopaling almost didn't made Smash 4 (and it shown in places), so if a reccuring & quite populars characters(I remember Bowser Jr was quite high on peoples most wanted list, pre-confirmation) like Bowser.Jr had problem getting to Smash 4, imagine Jon odds of making it over others characters of his own series.
And yeah, I knew about the MvC3 costume, but again, compared to other Darkstalkers character, it's still quite low imo. Not as low as sayyy, Rikuo or Sasquatch, but it could be better. (like Lord Raptor as apparear in every Namco X Capcom/Project X Zone game as a antagonist, yet Jon didn't apparear in person for some odd reasons!)
I swear i'm not trying to be a **** to Jon, but I just don't see him in the same rank as Jedah, Dimitri, etc...I love for him to get in Smash & finally get the love he deserve, but if he get in, I won't say it was because he was loved by many peoples working at Capcom beforehand.
EDIT: Also, when did I say he never mattered? Think closest I said is that was always quite a low profile characters compared to others when it came to appareances in various games, not that nobody on earth cared about him.
