Necrozma isn't "evil". I don't think it can really make conscious decisions. It's an animal, and it just so happens it's an animal that can control light and is incredibly powerful. In it's Ultra form, Necrozma actually does speak, but little more but blathering on about light. Certainly doesn't seem like a stable ally as opposed to Mewtwo or even Giovanni. Of course, Giovanni is little more than a yakuza boss at best. I don't think he was really too concerned with taking over the world (Until he discovered the Ultra Beasts- but even that is some time from happening, considering this take place before B2/W2, in which he appears as a challenger in the PWT), but perhaps he would be interesting in the monetary gain from selling off Eggman/Wily technology on the side and also giving the Cabal insider information.