If we're going to have overarching villains in the TDM setting, we should make them reasonably grounded. Even if they're magic wielders - or should I say, especially if they are magic wielders. Overwhelmingly powerful magic and overwhelmingly powerful mages tend to be a bit of a "game breaker" in virtually any fantasy setting, so keeping magic powers subtle is important, IMHO, even with powerful alchemists, or mages, or whathaveyou. (On that note, this video is quite excellent.) Also, we don't need TDM to ape the characters of the Thief series, including the main vllains.
I think a good twist on the "evil mage" archetype would be having the occassional mage who is a good guy/gal in essence, or at worst morally gray. There hasn't been much specificity about magic in TDM's setting, but from all the FMs I have played so far, the vast majority avoided going overboard with it as an obstacle for the player or as a storytelling element. About the only generalisation of depicting magic in the TDM setting I can think of, are that the pagan tribes use variations on folk magic or animistic rituals. I have not played a single FM involving the TDM version of mages, so I don't really know what yet their faction is like. Are they fireball-throwers, are they elemental mages like the Hand Brotherhood in TDM, are they quasi-scientific "mad scientist" type alchemists ? I think we need more context on the faction and how it's depicted in FMs, before coming up with any overarching villains.
For the aristocracy, making up a major villain is easy: A heartless, self-centered aristocrat with ties to the mob. For the Builders, you can have a severely corrupt and secredly decadent Bishop, who doesn't even take the faith all that seriously. For the pagans, you can have some warlord chieftain with a knack for bloodlust, cunningly uniting some local tribes to do raids and ambushes on the more civilised folk. For the Inventors' guild, you might have a brilliant mind who is either too naive or too jaded to realise he is selling his potentially harmful inventions to the highest bidder, regardless of what the consequences could be. For the mages ? Who knows ? You could have a villain for them, but we need more context about what their faction is like, for good or bad.
Springheel mentioned in the past that one of the main efforts in TDM is to keep the setting grounded and avoid making it over-the-top, including over-the-top humour and characterisations. Creating a super-nasty villain carries a bit of a temptation to write him or her in increasingly exaggerated ways. Whether that be insane cruelty and callousness, or things always panning out well for the villain, regardless of actual context.
In Thief, you had positive and negative traits in each faction, very often in the same individual characters that represented these factions. It added some complexity to the setting and its conflicts, rather than just having everyone as a scenery-chewing, one-dimensional stereotype. (Admittedly, the main villains were closer to that, but then, they were all insane megalomaniacs, so picking bits of the scenery from between their teeth is par for the course... )