I actually liked Zelda II significantly more than the first one when they first came out. If anything, it is one of the most underrated games ever released by Nintendo. Today, I find the quality of Zelda 2 to be staggeringly higher than the first Zelda. After playing the games again on 3DS, Zelda 1 isn't even playable anymore (I don't know how I could even stand this game as a kid, let alone enjoy it) - whereas the second offers a very rich (and much smoother) experience that is only rivaled in Faxanadu and Dracula's Curse.
The sequel I found most disappointing on a Nintendo console was likely Castlevania II: Simon's Quest. It was really vague, I remember not knowing for months how to cross that damn acid field, and using the stake on the orbs was weird. You essentially needed a guide of some sort to finish it.
Overall - Chrono Cross-
Chrono Trigger was one of the most brilliant and forward thinking RPGs in history. It had the best ATB battle system ever, which allowed for areas of effect, sacrificing mana + character moves to use spells/techs that were more powerful or had wider area zones. Most of the battles were scripted in, in a time when random encounters was the only good system (sure there were encounter systems like "Mystic Quest" and Lunar, but they were Inferior to even random encounters).
Chrono Cross was a greatly inferior version of Xenogears: Xenogears light. It also had a crap ending. Chrono Cross was an alright game when compared to Breath of Fire 3 and such, but it was a highly disappointing sequel to perhaps the greatest RPG ever made; the SNES version of Chrono Trigger.