Well, I personally prefer that they stay out if they can't work on the 3D version without a dramatic overhaul or cutting the AI partner system, but if I absolutely had to include them, this is my idea:
Take both Climbers, and glue them together so that they can't de-sync anymore (like how Duck Hunt has the dog and duck always together after any knockback an they never separate), strip the AI off of the NPC Climber, and just make them a duo character where every attack has a permanent double-strike hitter to keep the teamwork aspect. This way, you can keep both Climbers together without forcing Popo and Nana into alts/clones of each other, they still maximize their fighting potential by keeping the input-mimicking (although this would be fabricated due to the NPC Climber not having AI anymore; it would just be that every attack has both Climbers doing the attack.) and there's no issue of IC's Specials getting borked from an accidental de-sync. Also, glueing them together means they could get some new normals and specials that have both Climbers doing a team attack instead of just the usual "one-after-the-other" animations.
That all said, I would still prefer that they sit this one out, and hopefully can come back in full force for the next game(s) with their moveset and quirks intact.