My brother preferred the original over the second as well. He liked the story better (thought the second one got too convoluted) , thought it was too easy , thought that the game put too much emphasis on reaction commands , and didn't like most of the worlds/missions as much.
Out of what I've played so far , I was a little annoyed at how much tougher Cerberus was compared to Clayton/Chameleon , considering that the Coliseum was a 2 star world , while Deep Jungle was 3 stars.