The first Suikoden was the best. It was 15 hours long and felt like a weighty war epic. Lots of major character deaths. When you escaped from the crumbling castle and the montage of all of the character endings played with the mournful music playing, it felt like a lot had happened. There was a lot of sacrifice and loss to change things.
S2 is technically better (no more inventory micromanagement issues, better balance, better art, etc). However, Suikoden II was a 40 hour long game but only like 2 guys died, so when the ending montage plays you realize that pretty much everybody survived and lived happily ever after. It also retconned a couple character deaths from S1. It feels like the series got tamer as it went on. Then you reach S3 which was 65 hours long and literally only one guy died (during the first 5 hours) and you probably didn't like him either. The games got increasingly bloated but it felt like less and less happened. S5 killed more people off again but that game didn't feel weighty like S1 did.