Multi-target abilities are much more punishing than single target ones . . . If you find a villain overperforming because of these abilities, remember that you don’t have to affect every target you could
Also, you simply flat-out don’t have to use a villain’s ability if it’s proving too challenging for your heroes. (E.g., If the heroes are getting utterly swamped by the villain’s multi-target Pulsar Beam Projector, you could take a turn of the villain just monologuing about how weak their nemesis is while taking a basic Hinder action against them.)
A few villains have access to very powerful healing abilities, with the Domain archetype being the worst offender. Be careful about using these abilities to stall out the heroes until the scene tracker expires, as it can easily feel like robbing your players of a hard-won victory.
True, although this does make me get the idea for a villain whose entire gimmick is stalling. The Adhesivist, for instance, would likely have only abilities that Hinder.
Your musings on lieutenants led me to wonder about scenes that are all (or mostly) lieutenants. My first instinct is that that’s a bad idea. When 
= 4, for a hero team facing only lieutenants, the book recommends × ÷ 2 = 8 lieutenants, or 2 per hero. Unfortunately, I don’t believe I have enough play experience to judge how difficult that fight would be. At = 5, it’s 13, which is almost certainly too much. If we replace one squad of lieutenants with an environment or challenge, it becomes 6 at = 4 and 10 at = 5.
[Environments] are unusual because you’ll never use more than one in a scene unless something very peculiar is going on - maybe a string of major twists throws all participants into a whole new environment mid-scene?
Other possible peculiarities that could produce such a result include
- The scene takes place in two wildly different locations simultaneously, with villains and/or heroes constantly moving betwixt them. Teleportation would likely be involved. (In this case, I’d only count one environment when budgeting the scene.)
- One environment is the actual location where the action is taking place, while the other is a powerful entity (e.g., OblivAeon). (In this case, I’d count two environments when budgeting.)
- Both environments are actually massively powerful entities clashing with one another. (Ibid.)