Chrono Trigger, RE4 and Uncharted 2 are all pretty obvious picks I agree with.
One game I think actually has great pacing (especially considering it's subgenre) is Castlevania: Aria of Sorrow. You're never in one area of the castle for too long, and none of the sections in the game ever feel like a complete slog to go through. Even considering the nature of the Soul System, using it to it's advantage never feels like a grind (a trap that sadly, Dawn of Sorrow falls into). Boss encounters are designed just right; They aren't the damage sponges they are in Circle of the Moon, but they aren't disgustingly easy like the ones in Harmony of Dissonance. The castle design is better about directing the player to make sure they dont get lost, yet it never feels like a linear experience, or that you're being guided along. It's pretty easy for a Metroidvania to be filled with needless filler, but Aria always moves you along briskly, finding a great balance between uncovering new plot elements, boss encounters, and gaining new traversal abilities at just the right times.
It's one of the few Metroidvanias I can replay without having to go "Oh, now I have to play this part again...". Even Super Metroid and SoTN, arguably the peaks of the subgenre, have instances of that for a lot of people (Maridia and Inverted Castle, respectively).