DQ6 of course had the split world thing like Chrono Cross, but didn't explain jack shit about it, and it even had a neat little twist regarding the intro...but again, "its Dragon Quest" sort of spoils any sort of resemblance of maknig it decent cause the execution is that dreadful and it puts it on such a bare minimum level.
Say what you will about Chrono Cross' plot and its convoluted fucked up nature and everything, at least it made an EFFORT to explain its Split world shenanigans and all the shit surrounding it. Oh sure, everything about that may have been a lost cause given the direction they were taking, but at least they put a semblance of effort into it. DQ6 just sort of said "ho hum its there because...it is."
And DQ3's potential was...uhh...basically, its entire twist is "HEY GUYS! ITS A PREQUEL!!" There's nothing remotely interesting beyond that. Its a macguffin driven story that goes nowhere, then when you beat the alleged villain, the game shoved on an extra whole world map section that, from my recollection, has NOTHING TO DO WITH THE REST OF THE GAME, and basically exists to link DQ3 with DQ1/2.
...so yeah, DQ4 is about where the "wasted potential" thing kicks in. DQ8 as usual is a freak cause it at least made some use of its potential (actually, its plot wasn't even half bad. its issue, of course, is that the plot takes FOREVER to actually manifest itself)
And yeah, it didn't have to be Final Fantasy so much as I believe when CK said it, he was more acknowledging that Final Fantasy, being the other big jRPG series, tends to have at least have a decent level of execution to make its shit work. You could insert stuff like Wild ARMs, Tales series (...when its acknowledging stuff exists BESIDES Tropes...), Suikoden, etc. and most of them could have pulled off DQ5's plot in a way that would be rather strong and memorable...
...basically, interesting plot put into the worst possible series to make it clear, and its strong example of how Good Ideas are completely meaningless without a decent execution to go with it.