I completely agree. The card-based battle system put me off at first, but after buying the game, it really grew on me.
A couple other personal favorites are...
Skies of Arcadia - The depth of this game is amazing, one of the best RPG's I've ever played. It never really got boring at any point, and with a large amount of sidequests, it kept me playing for quite some time.
Golden Sun - Yet another game with great depth and memorable characters. The puzzle solving was very fun, though it got a bit tedious after a while...
Final Fantasy VII: Crisis Core - Although short in length compared to other RPG's, the storyline kept me hooked. The Action Combat system was enjoyable, and the main character is very likeable. Probably the best part, however, was that even though everyone knows what happens at the end, the presentation was amazing and highly emotional.