Considering the 3rd parties we've had have expansive gaming history, I DO think that it should be a very particular process by which they're added.
I'm not against Shovel Knight, but there are plenty of characters who, if going by gaming history standards, should be in before him and several others. Next in line, in my honest opinion is Snake. Metal Gear, Kojima and Snake have an incredible history in gaming, and have had appearances on Nintendo consoles. Something that each 3rd party has had.
If you boil down every 3rd party to that standard, it's not really as wide a margin as many think. Snake is a gaming icon just as much as Sonic, Mega Man and Ryu are. If you need evidence, just look at the social media buzz on MGSV. The hype that surrounded that game was immense. It's a series that came out way back when, around the time of Mario and Zelda, and it still has released stellar installments.
The problem I have with the "relationship with Nintendo" argument, is that it's used in no consistent way. Sonic has a "close relationship" because he's rivals with Mario. Let's ignore his history elsewhere and say that's the reason he got in. Not the legacy he created throughout his own history. Lets say that Mega Man ONLY got in because he appeared on Nintendo consoles, and not because he's a gaming icon that has spread to other platforms and created his own legacy.
Let's ignore the fact that a majority of Pac-Man's years...he's had very little to do with Nintendo. Pac-Man is a gaming icon from the arcade, to his worldwide popularity...that has nothing to do with Nintendo. Ryu has SF2 on NES, but what about the legacy of Street Fighter? It's had massive success for such a long time...and it only has a few games on Nintendo consoles. Historically, Street Fighter is massively successful in the gaming industry. The only part Nintendo has anything to do with is SF2. Yeah, his moveset takes inspiration from that game. But without the other games, Street Fighter wouldn't be what it is today. Nintendo can't take credit for that.
My point is, that every 3rd party so far is the creme of the crop. The series has appeared on Nintendo consoles from time to time, but Nintendo didn't make them who they have become. They've created their own legacy.
Snake has mainly appeared on Sony platforms. However, Ryu is pretty much the same way. You can't use it against one and not the other...especially when the other is currently in Smash, and the one has already BEEN IN Smash. Metal Gear is a AAA series that has stood the test of time and is legendary by gaming history standards. Hideo Kojima is a gaming legend in a similar vein to Miyamoto. He isn't the exact same to Miyamoto, but Kojima has contributed to the gaming industry in an amazing way with Metal Gear.
It's not about "repping" a company. That's not how things are decided. Sakurai doesn't sit there and think, "How can I represent X company with a character?". No, the character stands out on their own. Which characters/series have placed a significant impact on the industry in such a way? When you place characters in that specific lens, the choices go from "anyone under the sun" to "a small group".
Everybody has their favorite character, and that's okay. But to line up certain 3rd party characters with the likes of Sonic, Mega Man, Pac-Man and Ryu (or Snake for that matter) and justify their inclusion because they have Nintendo releases is asinine. There is so much more to it than that.
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, outside the context of Smash, Metal Gear and Snake are waaaaaaaaaaaay more well known than Layton. It's not even close.