Nightcrawler does not appear to be Catholic or religious in this version.
In the third season, a new original character, X-23 debuted. X-23 was the brainchild of Craig Kyle, Marvel's producer over the show. One day he told the producers and writers about his idea, and asked them to work her into the series. Like many other characters originating in comic book media adaptions, X-23 would later be adapted into the mainstream X-Men comics.
The writers of the show have admitted that they were big Buffy fans. Using Shadowcat as the catalyst, the two shows, Buffy and Evolution, are uncannily similar. A teenage girl with super powers fights bad guys at high school, while she attends classes. Buffy/Shadowcat have opposition against her with first the school principal and then the city mayor. Coincidentally, Joss Whedon, creator of all things Buffy, admits that he is a fan of X-Men, and based the character of Buffy on Shadowcat, even giving her the surname of Shadowcat's team leader: Summers.
The character Spyke is not a part of the comic book based Marvel Universe and was created solely for this show. Unlike X-23, he was never adapted into the comics later on.
According to Producer/Writer/Director Boyd Kirkland, the Acolytes provided new, bigger challenges for the heroes to face. The theme of the series was growth, beginning with these guys first discovering their powers, and then learning how to use them while still trying to get along with the "normal" world. According to Kirkland, by season 3, they knew they had to up the stakes. The Brotherhood hadn't really developed into the kind of team Magneto wanted, so he recruited Gambit, Colossus and Pyro. The first two were very popular X-Men characters in the comics, and Kirkland and co. wanted them in their series. But we already had many more heroes than villains, so the writers and producers thought it would be fun and more surprising to break with convention and introduce Gambit and Colossus as bad guys. However, these two would be conflicted about what they were doing, and would eventually join the X-Men. According to Kirkland this is one of the stories that never got to be told.