After many years I've settled on FF4 as being my favorite of the FF games. Pretty solid story, and after all the games that came after it, _not_ being able to customize and cheese out my party is pretty cool. Also, swapping lots of characters in and out of the party for story reasons and having the party actually feel different means that story and gameplay are joined for once. Five character party--yes please.
Chrono Cross I wanted to like, its story did feel pretty compelling, but I hated the combat system badly. Felt boring and time consuming, and the early game was so bad at it that I couldn't get anyone else to get to the later parts. It's also the game that made me hate thief classes: stealable items were so valuable and so omnipresent that it felt mandatory to have one of the like...two? thieves in your party for every boss.
Secret of Mana...I agree seems like the strongest, and even though I liked SD3 it somehow didn't keep the epic feel. I couldn't really identify with the characters, balance was waaaay off (looking at you, Kevin), and the leveling system was a distraction. Evermore gets more hate than it deserves, the writing was for younger audiences but it was still solid.
Star Ocean 1 was really, really good, and was also entirely inaccessible to western audiences until pretty darn recently. I'm sad that I can't play it on real hardware; it's one of a tiny number of games that my SNES flash cart can't handle.
Need to force myself to play FFT one of these days. The early game difficulty was a big turnoff, I liked FFTA though. Similarly I need to force myself to actually finish Ogre Battle, every time I try I wind up halfway through with a party that just doesn't feel like it can go the distance.
Could someone recommend a good DW game after 4?