Hey there,
Long time Champions GM here too. My current group, however, has never played champions (a couple made characters once, and some hero system Shadowrun but not Champions). While I lack the experience of many here, I have only run through 1 session with 5 players, and thinking about Villain teams just the other day I want to give a couple opionions based on what I saw so far.
Overall, I was surprised at how slow SCRPG ran. However, looking back I think the pacing issue was due to new players playing new characters. It took a bit for some of them to wrestle with the concept that they really could come up with anything they thought their character should be able to do based on a few vague words on the character sheet, and the flavor and description and being true to your own concept was king.
Also a few players were purposely feeling things out. Doing basic actions where they normally would probably have done with of their abilities. Just to see how the system works.
This led to most of the team, for most of the session to be focused on what they themselves could do, and not what others could do and synergies. The action scene I had them encounter was a bank robbery, that had a 3 step challenge in order to get into the barricaded and locked down vault where the villain was gathering loot for their escape. They dealt with minions and lieutenants and learned about environments that sometimes help and sometimes hurt. But this was a great learning way to divide things up, as when they got into the vault and were facing the villain + some D6 minions they had formed some ideas, and started to work as a team...
While they didn't take advantage of all the possibilities, what happened next was a sweet 3 person combo with a 4th being a support. One character boosted the entire team while hindering themselves, which kicked off the next character doing a red ability to hinder all the enemies, which led to the third character making an attack that was amplified by boosts, combined with the support having galvanized up, while the support took care of all the minions by taking their hits and redirecting them back. It ended up being a big move which resulted in a lot of damage to the villain and wiping out all 5 minions.
The villain bounced back after that making it a fight, and the whole scene ended with 2 heroes being out, and the villain going down on the very last attack on the last hero's action.
But how does this apply to a fight vs a villain group? Well I am hoping that if the team can focus on a couple villains rather than split between a big bad, a couple challenges, minions, lieutenants etc, that the players can learn some killer teamwork moves between their characters to be able to really push the damage levels up. If the team doesn't have abiliites/actions that synergize well with each other I am sure they would struggle, though. And I definitely worry about those fights wearing out their welcome.
I do remember a few champion groups having to be taught 'the hard way' how well teamwork can impact the results of a fight. Usually by facing a villain team that worked really well together but are a bit underpowered compared to the heroes to make them think "Why are we having so many problems? Look what they are doing! We should do those things". I am thinking this current group might just naturally fall into some teamwork, and it feels like SCRPG really lends itself to big team moves.
So I am hoping that player teamwork can make the fights a little quicker. 3 hours for a SCRPG fight and it sounding like it's about half over scares me a bit. I am not sure when I am running SCRPG again with our group, like other groups COVID has slowed things down, and we don't all enjoy Roll20. But when I do I will make a super villain fight the main part of the session and time it and report back to what happened with my group.
I do fear even with teamwork and big hits that it will be a slog like you are reporting, but we will see.