Mileage varies in that point. Besides, what are the sales figures on some of these games? My point isn't trying to look at cult-value... Atlus, Level5 and XSeed *does* make interesting games, but....
...and, wait a minute, in talking of visual aesthetics, I'd actually chalk-up Layton to French animated stylings way more than Japanese (which could be a point of appeal for non-J-ers).
FF9 still tried to retain semi-real elements that could be interpreted more "cartoony" than necessarily anime (you see the especially with Steiner and various NPCs - those who don't fit typcical "anime" conventions).
I wasn't looking at cultishness exactly. I guess I was making the same point as you using different examples, in that people look at the cutesy, "generic" jrpgs and roll their eyes, but will look at other Japanese stuff that branches out or seems a bit different. I think 999 is probably the example to that observation - it succeeded despite looking very cutesy in the character design.