Oh, you silly boy. You sweet summer child. Remove Donald and Goofy from the equation and the entire tower falls. On a fundamental level, this series can only function with Donald and Goofy guiding Sora from world to world. It might not seem so obvious, but when you pay close attention, you'll realize that it takes all three members of the trio to successfully enter each Disney world seamlessly, and this is because Sora, Donald and Goofy are all DIFFERENT from one another, and Sora is TOO DIFFERENT from each Disney world to just walk around and seem normal.
If Sora, Riku, and Kairi were to visit a new world as a trio, they'd likely all approach it in a unified way. Riku wouldn't ask too many more questions than Sora, and Kairi wouldn't be any less trusting of friends or foes than Sora or Riku. They all have similar backgrounds, designs, and attitudes toward new locations.
Meanwhile, Donald is almost jaded, is very eager to get down to business, and has a bit of a mean streak. He doesn't mind blowing some citizen off if it means he can get closer to what he wants or needs. Goofy is a bit more aloof, but also gentle, and less goal oriented and more empathetic than Sora and Donald. It's only with Donald and Goofy's support that Sora can realistically go about confidently in each world.
DDD showed us what it looks like when Sora strikes out on his own, and we ended up losing a lot of good pacing ingredients. Sora immediately befriends every ally in every world without a second thought, when this process usually involved a very light amount of discourse in previous installments. Sora had to be led by denizens of each world instead of by his own decisions, as Donald and Goofy usually would throw in their opinion and the three of them would agree on how to proceed in a situation. Worst of all, we had so many scenes of Sora talking to himself to expose information and his own opinion about events-- SO MANY SCENES OF THIS. Sora scratching his chin and talking about how each experience made him feel, or talking about what he has to do next. It's awful and not fun at all to watch.
If Sora is meant to represent the player in some way, and the Disney worlds are the destination we want to get to and experience, Donald and Goofy are the transportation TO those worlds. Sora can be silly with Donald and Goofy around, he can have fun, because they ARE silly characters, and in Disney worlds that are as full of levity and laughter as they are Heartless and villains, flexible characters who can both have fun and grit their teeth in serious situations are a NECESSITY.
I like Riku and Aqua as orbiting parallel characters to Sora, but watching Riku and Aqua travel to Disney worlds is a horrid experience. They are too mature and in their own heads to meld into Disney worlds and fit in. They exist as outsiders from the moment they land in a new world, to the moment they beat the final boss and have to say goodbye. It feels like you go through an entire setting without really having made any friends, and in a CHILDREN'S VIDEO GAME about FRIENDSHIP and LOVE and HEARTS you NEED a character who can CONNECT to other characters.
This is a difficult task even for Sora, the best original character we have for the job, and Donald and Goofy make the critical difference in achieving that bizarre-but-it-actually-totally-works balance that KH1 and KH2 (and soon KH3) hit in each world. So even though Donald and Goofy don't play giant roles in the fate of the KH universe, they make the VIDEO GAME work as a piece of entertainment, which is more important than a thousand keyblade wars.