I absolutely love the card based battle system, it was great in CoM and fully realized in Re:CoM. Definitely one of my favorite battle systems, if not my favorite. It's a system that really rewards your investment in it. If you just throw in some cards and a few cure spells (what I did back when I was 13 and just got the game), you get your rear handed to you.
Yet, if you really invest your time, buy cards from Moogle Rooms frequently, spend levels on CP, and slowly work your way up to only having high-numbered cards and the best damaging ones, you can really gain the upper hand. It's a good contrast to KH1/KH2, where one of the only ways to beat a boss you were stuck on was to go outside and smack Heartless til you were a few levels higher (like most RPGs, I suppose), where in CoM, you can spend levels on HP to survive longer, or buy CP to get a few more good cards in there, or maybe replace some low numbered ones with high numbered ones, perhaps get a few more zero cards in there to defend against big attacks, or you could even invest in some new sleights (though that's something I've never done).
It's a brilliant battle system and it's incredibly intuitive and fun. I really feel like everyone who complains about it really hasn't given it a chance/invested their time in it, or just blow it off because "it isn't Kingdom Hearts." But, everyone's entitled to their own opinion.