I'm not sure why you say Odin is like Hermes/Mercury. Odin is like Zeus but a bigger deal. He's a Sky God like Zeus, and is the ruler of the Pantheon like Zeus.
Historically, the Romans identified their god Mercury with the Germanic Wotan/Woden/Odin. Jupiter (also identified with Zeus) was made equivalent to Thor.
This is preserved in the English weekday names, which are equivalents/translations of the Latin ones used by the Romans; "dies Mercurii" (day of Mercury) became Wednesday (Woden's day), while "dies Jovis" (day of Jupiter) became Thursday (Thor's day).
Yes, Odin is the ruler of the pantheon, but Thor is the thunder god so he got the identification with Jupiter. The Mercury/Odin connection is their roles as gods of knowledge/secret knowledge/magic.
Odin isn't really primarily a sky god anyway. Knowledge/wisdom, secrets/magic/writing/runes, war/battle fury/victory, and to some degree death ("god of the hanged" and collector of dead heroes in Valhalla) are more central.