SMRPG is tied up with Square-Enix. The fact it was just Square back then may make the untangling of the contracts a bit messy. Geno still isn't in Smash.
EDIT: I'd imagine the same is true with DKC and Rare.
Umm, SMRPG and DKC have been on the Wii VC, Wii U VC and SNES Classic. Geno has been in Smash as a Mii costume and spirit...