I'll second Star Ocean.

I feel Kingdom Hearts is the most obvious choice as well. It started off promising and then went off rails really badly.

Metal Gear was also suffering from this as well. I never felt like it recovered completely after MGS4.

SaGa is another, though its unique in that the writing isn't necessarily bad, as much as its inconsistent to narrative norms due to the nature of the games. Romancing SaGa 1 and SaGa Frontier 2 could have been really strong titles had Kawazu made the narratives more focused and consistent.