Breath of Fire 3 has a pretty awesome fishing side-game. The main game has nothing whatsoever to do with fishing and if you were to play the game without taking an interest in fishing then the only reason to play it would be to catch the uber merchant fish 'Manilow' (IIRC). The fishing game is good though, there are a variety of floater/sinker/things and tons of fish. It's well worth a try
BoFIV for that matter, had an awesome fishing game, that took into account location, bait, and rod(for casting range and line durability, at least). It had a very large(close to 100, I think) variety of fish(granted, most of them were palette-swapped, but still quite a few), and almost every single one of them could be used as an item, many could be traded to certain shops for items, or you could just sell them for cash(making it, technically, "commercial" fishing
). One of the game's "Masters", who you could have your characters train under to gain skills and stat bonuses, requires fishing to train under(note: that particular Master gives rare items, not skills, as rewards). Even after catching every single fish in the game, including the largest size for quite a few of them, I still hadn't reached the third goal for him.
The series had a super-capitalist fish-race called the Manillo, so that might be what you're talking about.