Bubble Bobble, Castlevania II: Simon’s Quest, Metroid, Maniac Mansion, Dragon Warrior, Super Street Fighter II, ClayFighter, Nobunaga’s Ambition, and many others had multiple endings LOOOOOOOOONG before Chrono Trigger did. Hell, Body Harvest probably even had multiple endings and that was an Atari 2600 game. Check.
If you want to talk about plot-related sidequests or character development, Maniac Mansion did that way before Chrono Trigger. If you bother, you can learn a lot of things about many of the characters in the game. For example, when you microwave Weird Ed’s hamster and give it to him, which totally isn’t a necessary thing to do, you find out how much he loved that little hamster. Check again.
“Unique battle system!,” I hear some of you screaming. Well, Pong had a unique battle system, too. Big deal. Same with Super Mario Bros. Maybe you want me to limit myself to RPGs? Fine. Hydlide had a unique battle system. Check, mate.
Detailed graphics? I’ll bring up Body Harvest again. Sure, it had atrocious graphics, even for the Atari 2600, but is Chrono Trigger really that much better? Still with the 2600: you want detailed graphics? Pong. PONG! PONG HAD DETAILED GRAPHICS! The lines on that square and those two paddles were detailed as heck. Checkmate, mate.