The important thing which can be borne in mind is that, mechanically, all heroes are basically the same. Only in which level of ability the three tricks are linked to do they vary. So villains (and, by extension, all threats) can basically be defined by How Many Heroes Are They Designed To Fight?
I would assume that a Level 2 ability is the base for all types of villain. Whilst a more powerful villain might have a basic 3 or 4 dice attack, things starts getting awkward.
A villain that can pump out a 4 (or more) dice attack every turn is pretty dangerous, as at that level they could be taking a hero out each time. Even making such abilities limited use might not be the answer, if you give them too many uses. A 5 dice ability you can use six times per session is going to be quite deadly if there’s only three heroes; most fights will last less than six rounds, so the baddy will effectively get to use it all of the time (the heroes could play for time, I guess, but that’s a pretty risky strategy).
So, how do we make big villains without just upping their ability dice?
(i) More tricks – A villain with a 2 dice ability but who gets several rerolls during the fight is going to be more of a challenge than one with just 2 dice.
(ii) Strange Powers – Powers that limit the heroes’ ability to attack the villain will make him more of a challenge – a selected hero each turn attacks at -1, for example. Or allowing the villain to effect two or more heroes a round would be viable.
(iii) Increased Defence. Allowing 2 dice for reflex defences would make for a tough challenge. However the villain’s own base ability would need to be 3 or better for this to make any sense, so that the villain still has the ‘opportunity’ to switch to a powered defence.
(iv) Increased Toughness – Strangely this may be the easiest way to boost a villain without making him too powerful for the heroes to handle. He may only have a 2 dice ability, but give him a Toughness of 8 and he can win a simple war of attrition against a whole group of heroes. This may be the simplest way to tweak villains for hero groups of differeing size; two sessions ago the villain fought three heroes and had a toughness of 4. This time, against five heroes, he has the same abilities, but a toughness of 6 or 7. Toughnes isn’t how much health you have; it’s a measure of how important to the plot it is that you remain undefeated
Anyway, these are just random thoughts, and I hope they make sense to someone.