I haven't played this game since I beat it in 2003 and back then I really enjoyed the game even though I had problems with the game structure at times which kept it just short of greatness for me. But after playing it to the end again I had no problem with this stuff and can see why people consider it a cult classic. 
 
Most of my problems when I played it in 2003 were with the collection of pearls to get certain upgrades and I'm not a fan of games that force me to get collectables. But playing it now I realised that most of  the pearl collecting stuff relates to the story and are all missions that are as well designed as anything in the main game. 
 
So if you haven't played this game yet for some reason, what are you waiting for? It is only £6.49/$8 on PSN with the free PS plus membership everyone has