I still think that Banjo may have been planned for the base roster but was moved to DLC. Theres a few scenarios i came up with....
1) The deal with MS was late so he could have forced to them push back the release date, this is Nintendo's BIG game this holiday so that's a no no. They may have moved him to DLC to get everything out on time. Perhaps the Rare spirits were cut to avoid spoiling a Banjo reveal. We're not dumb and Sakurai and his team knew it would be obvious if Rare IPs appeared as Spirits but no Banjo that we could easily figure it out..
2) He was always planned to be DLC from the start to maximise profit for MS. This could be why "Minecraft Content" was rumoured for so long if this Minecraft boss doesn't exist it's possible that Minecraft was used as a code word to hide the identity of the character from potential leakers. They're both MS IPs so this isn't a stretch. It would even fit with Pappagenos' source's source who claimed they heard nothing in regards to Minecraft. Nintendo/Namco would use the code word amongst their own people so a MS source wouldn't know about that and only hear Banjo was getting in.. Rare spirits could have been planned but were cut, again as to not spoil a reveal..
3) Banjo was always planned as DLC and Rare was going to get spirit's in the game but perhaps they decided to only give them permission to use Banjo and that's it so any work they were doing on Spirits was nixed because legally they couldn't use those other characters.
4) Banjo's rights were given to Nintendo around E3 like Pappagenos theorized, Sakurai attempted to move a character to DLC in an attempt to make room for Banjo, Piranha Plant may have originally been planned for the base roster (this would explain the supposed cut 1st party character slot in the code, this would also explain why PP is practically complete despite being DLC) but they just couldn't get Banjo finished in time, so they end the roster with Ken and Incinoroar move PP to be a "free DLC" character and use PP as a safety blanket to continue work on Banjo. We're not expecting PP till February so that would give the Dev team extra time to work on Banjo we could see him release not too long after PP in that case.
In any case I theorize those Rare spirits were removed as to keep Banjo a secret. His inclusion would be huge, Sakurai, Microsoft, and Nintendo all know this.. we didn't see Cloud coming and I think they want this to be the same thing. A Banjo announcement for Smash would be like K. Rool 2.0 especially because of the background behind it all, the legacy, the current state of the characters franchise and of course a first party that belongs to rival console company joining Smash Bros. It has HUGE news potential. Nintendo and Microsoft would benefit off the press alone never mind the actual sales of the DLC which would only be helped by the hype and press..
I think there's more to all this than meets the eye, and like I said before. If Banjo wasn't meant to be playable than why not just give him a spirit? Surely Phil Spencer and Rare would have given Sakurai that atleast had they asked. Why wouldn't they have? Considering the presence of characters in the game that i can guarantee had a much smaller Ballot presence than Banjo. Rayman, Shovel Knight, Shantae, Dixie, krystal, Isaac, Geno all are present in one way or another and all of them were popular on fan polls the same fan polls were K. Rool, Snake, and Wolf dominated. The same fan polls people said were "bad sources to gauge ballot results" then we got K. Rool, Snake, and Wolf... and it would seem K. Rools number's were pretty accurate considering the royal treatment he's getting. Banjo was right up there with those guys and yet he's completely absent from the game in any way shape or form. No way.
Now we have Rare IPs showing up in the code. It's becoming painfully obvious that Banjo is on his way. Could I be wrong? Absolutely. My confidence in Banjo is where it was for K. Rool.. I am cautiously optimistic but when it came to K. Rool I couldn't see him getting ignored and I feel the same way for Banjo. I think he's coming. If I'm wrong then hey that's life. I have a good feeling about this..