Yeah, while I did enjoy Lillie and Nebby's story, it did feel more like we were just her muscle. Sure, we bonded with Nebby but I would've liked to bond with it on a more personal level.
I also don't feel like the multiplayer ruins how unique these legends are. You're playing alongside other people with access to similar Pokemon, it's not like they wouldn't use these Pokemon. They're also not even actually there in terms of the actual game, sure they're there but no one's going to acknowledge the other players unless they serve a function like the Pokemon Center. I'm also not sure how their ride forms ruin anything. Their bodies don't change too drastically and besides that it's not as though these are the first legends to be made rideable.
Though, this might be more because I'm thinking of what this implies about Koraidon and Miraidon and their lore. Of the rideable legends we have Solgaleo, Lunala, Latios, and Latias. Lunala and Solgaleo didn't change their forms. Only Latios and Latias changed forms and we've seen that it wasn't entirely needed for travel. The fact that Koraidon and Miraidon can change forms, adapting to whatever the player needs, and seem to be physically made for humans. Also the fact that they presumably do this when you help them after what could be a crash landing, it could hold a connection to their lore. Of course, it's equally likely that it was just a design choice.