Is the shin magami tensei series evil

It really depends on what you consider "evil" (i.e. if you're a Christian, probably... if not, probably not).

SMT games use a mythology which includes an Eastern interpretation of the standard Western religions. In other words, a parody. People will tend to look at them as though they promote Satan worship and wonton violence, but the games overall tend to have fairly positive themes, and there are *very* few instances of violence towards other humans compared to most other games on the market.

It's somewhat disturbing to me that the Grand Theft Auto series' two largest offenses had to do with story-relevant racism (Vice City) and sex (San Andreas), despite the fact that it keeps statistics of how many people you've killed just for fun. The only reason this question is getting asked about SMT instead is because GTA neatly skirts the religious issue. If you can accept SMT as an adult-themed, mythology based variant of Pokemon-style gameplay, then I don't think you could honestly consider it evil.

However, if you're the kind of person who thinks any mythological treatment of the Christian religion is inherently evil/paganistic, I would avoid it.