So, I'm rather late to this party. GAF + Internets always considered this game one of the PS2's classics, so I decided to jump in when I found a used copy at EB.
I'm relatively far into the game currently, and my impressions seem in line with many others. Environments rock, puzzles rock, combat sucks.
However, while the 'suckage' of the combat is the main complaint people have with the game, the issues it creates are still severely underplayed. I've enjoyed some of the AI of the enemies, but thats about all I can note positively. Compared to the inspired world, the black blobs are unimaginative. I've only run into perhaps three different enemy models at least so far, and I need to squint to tell much of any difference between two of them. The repetitive, bland attacks all done with one button are redundant, annoying, and, most importantly, not fun. I cringe each time I must enter battle. Perhaps this was ultimately the development team's choice; provide a stress on the player as he tries to solve the puzzles. If this is the case, I think this was a poor choice; the stress should come from the puzzles, not unexpected, simplistic combat where the player feels powerless. The combat issues have annoyed me to the extent that I currently can't bring myself to turn the game back on.
I've also had a good deal of trouble with the camera. I constantly find myself wishing for a first person view or behind-the-shoulder camera of some sort. Granted, the game released earlier in the previous generation when even the best developers could rarely nail a perfect camera system, but its difficult playing this after Zelda:TP.
A final, trivial complaint. It really bugs me that the girl is taller than the main character. Dragging around the tall girl and seeing the drag it causes to her body and the lag it causes in movement, while a nice detail, bugs me as I play. Minor, personal preference there, though.