Eh, Falco and Roy didn't have huge differences either. They're on the same level, really. Only Ganondorf, Young Link, and Pichu has major differences in comparison. They also had different bodyshapes in comparison.
Echoes still didn't exist yet, so it doesn't matter if he was "kind of" similar. It wasn't a thing till maybe 4(if he intended to have that idea yet, but Lucina and Dark Pit were just called clones at that point). Doesn't mean Dr. Mario would've made sense as an Echo. Another thing is that in 4, all the moves were literally adapted from one character, bar the Final Smash. Dr. Mario was a combination of Mario and Luigi instead. So there's some difference in creation, which could explain part of the labeling. Also, Dr. Mario got even more differences in Ultimate while Dark Pit and Lucina didn't, which may be part of why).