Great article and it actually made me think back to games I've previously played and how effective the various villains from the wide variety of games I've played over the years are and once I'd thought about Dr Nefarious, from the Ratchet and Clank games, I kept returning to him as a great example for the points you made and just as a great all-round example for an engaging and most important of all, a fun to fight against enemy.
Apart from the amazingly funny dialogue of the series, which extends to the protagonists as well, I think the one experience that truly bonded me to the character was the Qwark Vid Comics from 'Up Your Arsenal'; a collection of side-scrolling mini games starring Captain Qwark in his battles against the original 'non-robot' Dr Nefarious that effectively explained both characters back stories in one swoop.
But back to your points and this article:
Be onscreen Referring back to my point above, Dr Nefarious' screen time was mostly used by news reports, vid comics and 'Supervillain Weekly', explaining his villainous ways without the game having to come up with an excuse for him to meet Ratchet in person.
Do villainous things The list is so long and evil it'd be hard to know where to start...I still like him regardless
Be a character He turned to a life of mad science after being relentlessly bullied in school by Qwark who even thwarted his first evil plan and turned him into a robot. This is basically his back story and it works just fine for him to be motivated enough to want revenge on the world; he's a mad scientist, it's what they do.
Beating the villain has to feel good There has to be at least some satisfaction gained beating Nefarious at the end of UYA after he's turned one of your close friends (and a very funny character) into a robot and his downfall gives new life to the depressed Qwark.
Get your hate on early UYA starts with Ratchet finding out his homeland is under attack by the Tyhrranoids, a blow dealt close to home by Nefarious, and one leaving Ratchet, and hopefully the player, feeling angry.
Don't Just Take Them Out of the Plastic See my earlier point about the Vid Comics.
Another thing I liked about the character were his interactions with his butler Lawrence. The short cutscenes of exposition, normally Dr Nefarious finding out about Ratchet's actions, were brightened up exponentially by the sharp dialogue and satire of the two opposites.
PS. This is mainly about the Nefarious in 'Up Your Arsenal', which is in my mind the best Ratchet and Clank game easily and definitely one of my favourite games ever.
PPS. As Lawrence would say about Dr Nefarious: He puts the 'wit' in twit...