It's less about 'second class citizens' and more how indies really are their own thing. Think about this: why are indies successful? Because they offer something AAA companies do not focus on, so why would we want them involved in big AAA titles? Seriously, indies are best represented within themselves, not AAA companies. That's why Rivals of Aether and those of that nature are better choices for having indie characters repped in a fighting game/crossover title. Also,
EricTheGamerman
EricTheGamerman
had a good point: indies don't quite work like other character choices.
For example, AAA games often have multiple releases and many characters involved, yet still have a single favorite that makes it easy to pick from if you can only pick one to represent the series (Simon for Castlevania, Cloud for Final Fantasy, Ryu for Street Fighter), but indies not only have the issue of many of the characters being beloved within a single game but also the issue of many characters loved among indies as well.
Think about trying to decide just for Undertale, for instance: do you pick Frisk, Sans, Papyrus, Undyne? All of them could work, and they are all equally loved and people would be equally upset no matter who got cut, unlike with Simon when Alucard was an AT or Ryu/Ken when Guile was an AT. Now, imagine only getting one or two choices for indies as a whole...who the hell do you pick? Sans or Frisk? Shantae? Shovel Knight? Quote? Celeste? Meat Boy? Isaac? Cuphead? Hollow Knight? Insert like 10 or more characters from popular indies and you see the problem.
Now compare to Uncharted: who do you pick? Nathan Drake, obviously, no brainer.
Indies games are their own thing, and they tend to connect with us better because they are their own thing: not just a game, but a project with soul and heart crafted when the budget is lacking. Thus, I think they should get nothing but small nods from bigger names to keep them as what we treasure them to be. If anything, it's less about indies being 'lesser than' AAA titles, and more that they are the perfect reprieve from AAA titles and need to stay separated to enjoy them, if that makes any sense.