Indeed; it's been an often quoted fact that David Whittaker originally had Ben and Polly in the first two episodes of Evil, but had to remove them when they were written out in The Faceless Ones. Pity, it's the last time until the late Tom Baker era that the Doctor had three companions. It did allow adventures to be spread over 3 or even 4 storylines when everyone splits up.
I suppose splitting the companions into more storylines worked better when the actual stories were longer. But if you're just doing a 4-parter, too many companions can really bog things down. Three companions worked fine in the early years when it was Ian, Barbara, & Susan/Vicki. They clearly had it worked out what the dynamic was supposed to be between all of the characters. It doesn't work so well when you have companions that were just kinda thrown in suddenly because the characters proved popular, even if they don't mesh with the rest of the cast.