To be fair, K. Rool isn't exactly known for being a brawler, so I don't see why we can't have a Shantae Mii costume and a Shovel Knight Mii costume. Make perfect sense to me in that regard.
As for the second point, considering their obscurity and relatively lack of importance to video gaming in general as third-party candidates compared to the third-party characters we have had throughout Smash history, yeah, I'd say the representation of them via Mii costumes is most appropriate.
The problem is you're doing the number one must crucial thing that all Smash fans do despite Sakurai showing it's a bad idea to do.
Assuming he sticks to a strict set of rules when creating the game. I feel like Regina George anytime everyone is all ''BUT SAKURAI'S SET OF RULES...."
''WHATEVER THOSE RULES AREN'T REAL!"
No creative person sticks to the rules that much if the benefits of breaking said rules are greater than the benefits of sticking to them.
As someone who fancies themselves creative? I never would. I'd think hard about it, but I never would. And I've spoken to lots of different artists in different mediums who are very much the same.
Sakurai is an artist, by default we're born to break the rules, even the ones we've set if they're going to benefit something in the end.
And only Sakurai will known if he's willing to do that for SK and Shantae. And honestly considering how little he's said about third parties? It's kind of funny to be saying he's got a set of rules for them in the first place.
If Sakurai feels Smash will benefit from adding someone, no matter who they are? He's going to ****ing do it. No matter what he said a year, two years, three years ago or yesterday. People change their minds. Especially creative types.