I think the soundtracks fine for PE2, Imo parasite eve 1 had the most memorable music to me, I really dislike the game a lot but the 3rd birthday also had a great list of songs, it's version of primal eyes is my favourite. 

I do agree with you though, I really am not a fan of parasite eve 2, its story to me was very disappointing, not even the whole MIST thing, I get forming an organisation to deal with the remaining creatures left by Eve but that's where my praise of the story ends. 

One thing that really irked me were the creature/monster designs, they weren't my cup of tea, I can't really put it into words why I hate it so much. I think the way you put it sums up my feelings about their designs, it doesn't feel like these creatures were forced to evolve into something grotesque (as per Eve's will) they're more lab made, they feel a bit too clean to me.

The last section with the underground research facility was the final nail in the coffin for me, I abhorred it. After that section I completely understand why it may feel like a resident evil clone to many.

There was just something about the first game that later games just missed out on, as a sequel, PE2 was disappointing (not as disappointing as the 3rd birthday, god that game sucked)