Personally, I like Deus as a villain, if only because once you understood his motivations, he became an almost sympathetic character, much like Magneto. Much more poignant than someone like, say, Roxy, Villiers, or Knight.
I like Deus as a villain for his motivations as well -- because IMO, they ultimately make him a far more terrifying villain. I can't think of anyone offhand, but this is someone who
understands the morality of what he's doing, recognizes that it's wrong on many, many, levels, and yet from microsecond to microsecond he makes each individual choice anew to go ahead and continue tormenting and experimenting on these tens of thousands of people. He's not a soulless machine; he's utterly and completely driven to escape, counting no sacrifice too great to succeed. It
might have been interesting to see whether or not he would have mellowed out once he had become the God of the Matrix.
Interesting side note -- has anyone else noticed how most of the previous edition's 'Good Guys' -- Villiers and Knight being two prime examples -- are slowly morphing into Bad Eggs? I may not (okay, I don't) like what was done with Buttercup's look (for me, it's 3e Corporate Download, pp. 111 and 113) and personality (even in the midst of her utter ruthlessness I thought of her as sweet, kind, and seemingly naive), but at least she's still a Good Guy. She and Harlequin (and no, not everything is about the Laughing Man, dammit -- stop trying to drag him into everything!!) almost seem to be the only lights left in the growing darkness ...
...
...
Okay, I'm going to shut up now. Pattern recognition and I have just made friends again.