For me there are a lot of important things. I think first and foremost there is story, i like something that grabs ahold of you and doesnt let go until you finish it and revisit the game a couple more times.
But also I am on the boat with most who said that the best thing is a good combination of story, characters and battle system.
Like CO i am a big fan of Shadow Hearts because indeed, the battle system does not let you just sit there and press a button like other rpgs but doesnt let you full onto action like some rpgs tend to do these days. You can still have your strategy. Covenant showed you which turn was coming up next and during boss fights it was incredibly helpful because Boss fights were a bitch, they were not really that hard but they still gave you a bit of challenge sometimes. One of the things I like to do is ignore super items unless there is no way out. In SH there are items which let you spin the judgment ring many times, 3 or 5 or more. This means that you can potentially hit a dude 25 or more times and if you hit most of it in the strike zone you can do a whole lot of damage. SH is harder than Covenant and it really brings up its game, maybe Covenant was dumbed down a bit but is still a great game and...i completely forgot what this thread was about.
Anyway, yeah, its mostly a combination of all those things that really make a good rpg. Sometimes you can get story but lack in characters and battle system, like FF8 before mid disc 3 (I dont remember when it goes to shit but it does, Esthar?) and sometimes you get fun battle system, pretty graphics but a loose story and practically no characters like Legend of Mana, and these are still enjoyable games but you dont get me to suck cock for them like I would do for Shadow Hearts, Xenogears or Persona 2.
And sometimes, very rarely, you get a game which lacks main components and somehow ends up being fun. For the life of me I cant understand why I liked Arc the lad Twilight of the Spirit. The characters are godawful, the main dudes Kharg and Darc are complete douchebags, the voice acting is horrible, the battle system is so simple and unchallenging the first and only time you are gonna die is at the last boss fight, the graphics are not that special and its just a really mediocre game, but somehow I ended up greatly enjoying it. Maybe it was just Bebedora. She is utterly awesome.