The difference is Devoe is a metahuman, Adrian Chase was not. Adrian was just a guy who plotted things in advance really well to stay ahead of Arrow.
True, although now that the comparison has been raised, it occurs to me that they're similar in that their origins both tie back to the beginnings of their respective series. Prometheus/Morrison/Chase was "created" by Oliver's actions in early season 1, and the Thinker was "created" by piggybacking off the dark matter explosion.
Ooh, one more detail indicating that the DeVoes weren't exactly benevolent to start with: According to their dialogue outside STAR Labs after Thawne/Wells's press conference, they both were able to predict that "Wells" intended to cause an explosion that would create a large number of metahumans, and they were okay with letting it happen just so they could power DeVoe's Thinking Cap. That's a pretty extreme level of selfishness and disregard for consequences to others.