I'll be honest, I've only ever seen one instance where Sci ships/characters were in the majority. While in some cases, having the majority as Sci might be a hindrance, I think having a majority of anyone particular class can be a problem. In some cases, a Sci character can make it easier to make sure those optionals are easier to attain. For example, in Infected, using a combination of Gravity Well and Photonic Shockwave to keep the Nanite ships away from the Nanite Transformers etc.
Might be play style, but in your example, it's possible to do it that way, but not at all necessary. Simplest way to do that is just knock all 4 generators on one side to just under 10%, then blow all 4 at the same time. Everyone then pounds on the Transformer, and if you have decent DPS, the thing is destroyed long before the spheres wander over to repair it. You then just mop up and move to the other side.
Simpler, and doesn't require much coordination or special team builds to do. That's why it's the most common battle plan for that one.
Not that the other classes can't find a way to play a role, just that this is why DPS is favored so heavily; because you can wander into a new group (not a group that's from the same fleet and worked together), and there's an easy, straightforward way to make it work every time, as long as you brought decent DPS/survivability. I bring an Escort, and then split my skills between causing damage and surviving as much as I can. I can't take as much damage as a Cruiser, but can dish out a lot more.
SCI is looked down on a bit because while cruisers are all about tanking, and escorts are all about damage, SCI are somewhere in the middle, which means that they generally aren't really great at either, although they can certainly contribute, and a good build can overcome a certain amount of that.
Carriers get you better damage, but when you have specific mission goals, automated drones can be an issue. Like having your ship on autofire, or calling in photonic fleet, sometimes you need to STOP shooting at something, as most of the easiest ways to beat a space STF involve NOT blowing something up, but just taking out the support ships, or knocking the gate to 10%, etc.
Anyway, just different play styles, mostly. Main reason I stay away from SCI is that the BOFF abilities you get there just aren't as helpful to my play style as being able to pump lots of cannon fire or torpedoes out there, or repair my forward shield quickly...