I had to make that same choice back when I started buying pcbs, haha. I went with Viper New Version since I could play DX on my ps1. (Yeah I know, but when you're starting off priorties are weird that way)
DX has multiple game modes and tons of secrets, not to mention the fading medals which are a real nut-buster to maximize score. Very cool game and lots of depth and replay, it's definitely my favorite mainline Raiden game.
Viper Phase 1 is a bit more subtile in its game mechanics. Or at least until you figure out the secret to maximizing the medal count and turns your entire game strategy upside down. There's a lot more depth than is visible on the surface, but I wouldn't say it's as crazy as the DX medal fade.