I'm not really a fan of shmups, so Saga is far and away my favorite game in the series.
Last time I said that, I got a "but you can get an RPG anywhere!" as a response. This is true, but none like Saga. It really does a whole lot differently - notably, its battle mechanics are a lot more active than most, which I really like. It's also almost entirely devoid of filler (maybe that dungeon with all the one-way ramps coming the closest, but even that had a purpose in the plot), which, while it means it clocks at only around 11 hours or so, means it gets right to the point and never overstays its welcome (a la Portal). Plus, it gives you a lot more insight to the world of Panzer Dragoon, and that's a world that's worth that much insight. That's something Orta was able to provide more of, later, in a shmup entry, but since I'm really bad at the shmup entries, a lot of Orta's encyclopedia is still behind lock-and-key, while Saga is right there, available for me to pore over at any time.
I suppose its biggest flaw is, other than its obscene rarity, that it's too easy, but since it's an easy game I greatly enjoyed while playing, I can't hold it against it too much (I tend to lean toward easy games more than hard ones these days, anyway - not that I think hard games should go away, far from it).
But that's me, anyway. And I might just be feeling that way because I spent so much money on it. But whatever the reason, I really like that game.