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Anything associated with Breath of Fire and Suikoden tend to fall into this camp as fans adore these games but official reviews tend to fall into the "Good, but not FF good" which I always felt was kind of bulltrout. The Last Story is another title I felt never got the real appreciation it deserved, the game is certainly flawed but I felt it brought enough cool new elements to to stand on it's own merits.
The mainline MegaTen games also tend to be weird as The White Wizard of Fynn points out that the story heavy Persona and Devil Survivor series tend to overshadow the better constructed mainline games like Strange Journey and SMTIV.