64:
Top:
Watt
Bombette
High: Parakarry
Sushi
Mid:
Goombario Kooper
Low:
Lakilester
Bow
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TTYD:
Top:
Bobbery
Goombella
High:
Vivian
Flurrie
Mid:
Koops
Yoshi
Low:
Ms. Mowz
Factors Included: Access to AoE. Ability to hit different enemy types (eg. Spiked, Flying, etc.). Utility access. Availability is considered but not as heavily, considering how Sushi is a lot more useful against the numerous fire type enemies in Chapter 5 than Goombario is comparatively in the chapters he's in. Backtracking for upgrades/getting Ms. Mowz. For TTYD, durability also factors in.
Feel free to discuss/argue, since I'm a bit shakier on the 64 ratings due to not having played it as recently. Koops could probably be higher considering he's the only partner who can hit Spikey enemies until Yoshi which is like 2 chapters later and is the only AoE partner till Vivian, but he also has pretty heavy competition in the mid-late game considering just how good Bobbery and Vivian are and Shell Shield isn't that useful. He also has the lowest HP tied with Ms. Mowz and I don't think 1 point of Defense makes up for 5-10 HP.