You also have to consider that the best selling DK games never had Dixie Kong in them. #1 DKC, #2 DKC Returns, and #3 DK64. Then there's the fact that general audiences and just a lot of people in general see Dixie as a "female Diddy" sadly. You guys act as if Dixie is a shoe-in. Do we really know that? I'm certain the only reason K. Rool got in and got this much love is because he won the Ballot. If that's the case we better hope there is another Ballot and that the Dixie supporters rally behind her more than ever.
Weird that you have this impression that people see her as a shoo-in, because what I see is the opposite.
Post-K. Rool the hype went up considerably because people saw Chrom and figured that Dixie could perhaps actually be an echo fighter.
Post-Isabelle that hype died down a lot given it gives more credence to Vergeben who has never mentioned Dixie, and the case of Isabelle showed that Dixie would be treated more as a semi-clone than an echo, which, combined with the vergeben stuff makes it even less likely she's in the base roster.
So with all that in mind, no one is acting as if Dixie is a shoo-in. We act as if Dixie DESERVES to be in this game, which she does, but that's a different argument. You'll notice most people that love Dixie are already resigning themselves to having to campaign hard for her to have her hopefully be considered as DLC. What you said about K. Rool making in because of the ballot is also exactly what I was saying, even if you disagree with the reasons of why Country content has been pushed aside post Rare.
As for the Isabelle VS Dark Samus thing. Once again it comes down to the fact that Dark Samus has the same proprtions as Samus, and Isabelle doesn't have the same proprtions as Villager. Then add on the super popularity of Isabelle and it just makes sense.
This is one of those Sakurai explanations I don't buy. The difference in proportions between Smash Villager and New Leaf Isabelle is definitely there, but it would not have been that much of a reach for them to have the same skeleton, much in the same way you can rationalize Marth/Lucina and Roy/Chrom as having the same skeleton.
Isabelle could have very easily been an echo fighter, and I'm willing to bet money on the fact that the only reason she isn't is not because of design considerations, but because of business ones: wanting to make the character a unique fighter due to her popularity and high importance as a face of a highly popular franchise.
So sure, Dark Samus being an echo is not something that happened because she's not japanese, but its lack of uniqueness outside of aesthetics definitely makes sense as a symptom of a character whose developers probably didn't get the chance of having as much input in its design as those for characters like Isabelle.