Which Pokémon title was the first main-series game to feature a day-and-night system?

Pokémon Gold and Silver were the first main-series games to feature a day-and-night system.

Released for the Game Boy Color in Japan in 1999, Gold and Silver added a real-time clock that changed the game world according to the player’s time of day. Certain Pokémon, events, and encounters could vary between morning, day, and night.

The system was one of several major additions in Generation II. Gold and Silver also introduced 100 new Pokémon, the Johto region, breeding, held items, and the Dark and Steel types. After completing the Johto adventure, players could return to the earlier Kanto region.

Pokémon Crystal was an enhanced version of Gold and Silver, not the first game to introduce the feature. Likewise, Ruby and Sapphire continued the idea on the Game Boy Advance. The day-and-night clock is therefore a Generation II innovation rather than a feature of the original Red and Blue games.