I don't think PQ and EOIV have atmospheres that are directly comparable. Both games strive do different things, so it's not really fair to say that one is strictly better than the other.
EOIV is an extremely, extremely immersive game. The locations you visit are mystical-yet-grounded, so it feels like you yourself are trekking through forests, caves, etc. The dungeon music is pleasant, subdued and non-intrusive. There's a day & night system which gives you a sense of how long your given dungeon excursion is (which also lends to the immersion). Events are recounted to you by a narrator in a story book like manner. There's absolutely no banter between party members (or rather, it's for you to make up). EOIV is designed from the ground up to get you into a flow in which you get fully immersed into the game world. It prioritizes the players experience over the characters.
PQ on the other hand, is a different beast altogether. The locations you visit are bizarre and fantastical. The characters are constantly talking amongst each other or reacting to certain events or enemies. Dungeon progress is periodically punctuated by brief scenes skits or scenes. There are a handful of cutscenes. Characters talk and react to things during battle. Unlike EOIV, the game doesn't prioritize the player here; everything is set up to manipulate the cast in some way. Getting them to experience new things or even developing them in certain cases. It's all about the characters, rather than the player.
To put it simply:
Both games are trying to do different things. I don't think either game is superior to the other, so it really just comes down to taste. It's pointless to try and prop up one game over the other.