I really loved the battle system in this game. A strategy and set of skills was a key to succeed. Elements were absolutely important as not only more damage, but more turns you could get if using them correctly. Wrong set of skills could result in easily getting killed even by random encounters. What I didn't liked though, were the later-stages passive skills, that were making you immune to physical/elements/ailments ~ and only skills with 'Almighty' element were effective. ~ So later the elements were not important, as you could just simply use almighty skills, where it was not possible to have resist on that. The secret bosses were still a challenge there ~ but I'd rather say, that they were not that hard, but it took some time to kill them.
Skill Assignment System was a really nice feature in my opinion, because it forced players to think and plan a strategy ~ not just go to battle and have a wall of skills.
Personally I liked all characters ~ kinda except Sera ~ She was kind of boring and stuff. =P
The story is kind of weird ~ but it's really nice. The amount of plot twists in the second game is pretty surprising. I admit, that I felt kinda 'lost' sometimes and didn't know what's happening ~ but generally it's a really enjoyable plot.
I don't know about the references as I haven't played any SMT games besides Digital Devil Saga games, so it's hard for me to compare anything. =P
And the music ~ Now that's one of the things I've liked the most ~ It's absolutely great!
Despite the fact, that I like RPG's I can get pretty quickly bored of them. For example I've played FF X and FF X-2 ~ I've enjoyed both, but never managed to fully complete them. I just got bored of them for some reason. Digital Devil Saga however, I've completed both games and I really loved them. =3
These games have great gameplay, balancing (except end-game-skills), plot and music ~ Pure awesomeness. =3