Personally I feel that the game is open to all characters who have originated from video games.
Pokemon started off as a game right? The anime is based off it, not the other way around.
Digimon might be in a similar situation. A character like Augumon could potentially be valid if it initially started off as a game.
At some point a line has to be drawn, because there should be a theme. Goku or Dragonball has a ton of history with Nintendo as early as the Nes. However, I dont feel as though that warrants his inclusion into the game. While his character could be worked to fit into the smash universe, he is out of place because he doesnt share the same background as the others. Its what ties the game theme all together.
As far as other characters like Master Chief go, I believe Ultimate has open the gates for non nintendo related characters to join the fray. Its a celebration of gaming history at this point, and despite what some may think that easily extends past Nintendo's influence. That being said, seeing characters like Tracer, Master Chief, Dante,Nathan Drake, etc dont bother me.
As much as I hate Fortnite and Minecraft, they probably should be represented in some form.