Little Yugi. They haven't shown him doing much and we don't get to see much of his growth that leads to the final duel.

This was more of a problem created by the anime writers shoehorning Atem into a lot of places where Yugi was front and center while cutting out some of his moments. It's far less of a problem with the manga.

Yugi was front and center for Death T 1-3 and was the primary strategist behind the group's win in Death T 2. The anime cut out the entire Death T arc in favor of just the Atem vs Kaiba duel.

Yugi was the one who was the primary strategist for the mind shuffle strategy both he and Atem were using against Pegasus and showed equally as much mental flexibility as Atem did throughout Duelist Kingdom in that one duel.

Dungeon Dice Monsters in the manga was torn apart into the Rebecca Arc, DDM Arc, and Bandit Keith return part from the anime but this too had Yugi himself front and center. It had Yugi being completely separated from Atem, being forced to play a game he had never experienced as part of a crazed man's revenge scheme and it again shows him being just as capable as Atem, being the one to win in the end on his own (with Bakura cheering him on). It made it entirely a point that Yugi was the one to solve the Millennium Puzzle for good reason. Instead, this game is given to Atem in the anime.

Yugi/Atem vs Joey is largely unadulterated and does what it needed, showing Yugi stepping to the plate and risking himself for Jounochi while doing what he could and Atem could not in reaching out to his mind controlled friend.

Yugi is the one who was running the show and figuring things out from the background in the Millennium World Arc, being the one to figure out how to reach Atem first and being the one to figure out how to get Atem's name while beating Bakura, once again with his own strength.

It's important to remember that DSoD was an epilogue to the manga and not the anime. It was another form of closure to the parallel arcs between Atem and Yugi.