Kanto
As Ash was the only main character ingame, I had much rather he travel alone for the majority of the season, getting a companion in Saffron in the form of some new character.
Orange
Tracey was fine... But Misty again was reduntant.
Johto
Casey honestly had a lot of potential in becoming a companion, and Macey (Fire trainer who was crushing on Ash (was recurring character and technically a League Rival)) did too.
Hoenn
So much wasted here. Had Wally appeared, Ash had a companion who actually was new, and because of his game situation, he could have been the first Rival companion. Drew could have been good if there was no May.
Kanto BF
The lineup was ok, but I could have missed May and Max and replace them with Leaf.
Sinnoh
Ok. This one had me fooled that Paul would have travelled with Ash and Dawn because of merchandise. Dawn is fine, but I think that Conway and Barry could have been great mainstay characters for comic relief, as none of the other characters had much comic in them in DP/G/Pt.
Unova
... I think that Chili would have made a much better companion than Cilan, and that Bianca should have been travelling with Ash instead of Iris. Add Kotetsu near the League, and you have seriousness, comic relief, and whatever else you need. And Ash.