I'm a fan a both. I have tons of shooters on both the Saturn and PCE, and both have their time and place for me. The gameplay style is just different for each generation of shooters. With the Saturn a lot of games started towards the bullet-hell play style while the PCE shooters are more old school style with more enemy dodging and the like.
As much as I love the Saturn, the fact is that there are tons of great shooters that never came out on the Saturn that were on the PCE HuCard format, like PC Denjin, Magical Chase, Hana taka da, and the fantastic Soldier series. To me I love the gameplay, presentation, and music of these games despite the technical superiority of shooters on the Saturn, Dreamcast, PS2, PS3/360, iOS, etc. Those games will always be great no matter what else came out after them!