Gamasutra has a great piece about the design legacy of Chrono Trigger:
Within the dungeons in the game, the developers imposed linear structure through enemy encounters while giving players a great sense of freedom. This was done through the developers' choice to set up unique, handcrafted enemy encounters, which were attached to visible — and often avoidable — enemy avatars inside the dungeon.
Chrono Trigger’s non-random enemy encounters were a gameplay anomaly when compared to contemporary games. No longer were you penalized for exploring the game. Instead you were encouraged to find alternative paths within linear story-arcs.