The biggest issue people had with SO3 was mainly the plot twist, It was SO4 however that some various....characterization issues.
SO3 was one of the few localizations which had Alexander O. Smith involved with it's script and so it was competent in terms of localization and the gameplay was solid, outside the plot twist, SO3 is generally looked much more favorably compared to SO4.
I disagree with this. There were a lot of things wrong with SO3 besides just the dumb plot twist. Like how you spend the first 20 hours doing all this pointless, inconsequential busywork. Or the excessive amount of pointless backtracking (e.g. revisiting every previous dungeon with the ring of destruction, backtracking when that boulder blocks your path in the volcano dungeon, etc). Or the bland corridor-style dungeons. Or the item creation system, which is almost impossible to figure out without a guide and involves pissing all your money away/reloading over and over.
SO3 also appears to have completely shifted direction late in development in order to implement that big twist. Look at the country of Greeton.
- Nel originally rescues you because she thinks you're from Greeton and have access to advanced technology - must be a cool place!
- there is a gate leading to Greeton from Peterny, which is blocked
- various NPCs tell you how Greeton has rock people and featherfolk
- there is a cutscene where you discover an old ruined golem from Greeton
But of course after all that buildup, you never go there. I'm convinced the original plot would have you travel to Greeton, but someone at tri-Ace saw The Matrix and decided to change it.
But at any rate, I think it's unfair to say that most people who disliked SO3 just didn't like the plot twist. There were a lot of things wrong with that game.