I get it. This is a question that can't be answered. It is a game and it is a fun game. (If you don't like Armada, I can recommend some forums where you might enjoy reading more)
For anyone who has played this game much of all. Ship activations and activation order a a HUGE part of the tactics of this game. Why are Flotillas great because people are willing to buy them just for the extra activations. Why are life boats and relay annoying? Because it makes use of those ships we were perfectly willing to just buy for the activations in a pretty effective way.
But why are we so annoyed about these little flotillas being so good. I think it is because in that little part of our brain that likes to pretend we are actually commanding Star Wars cruisers in space naval engagements doesn't think these little support ships should work in our imaginary battle the way they work in the game.
And now we are back to activations. Of all the things in Aramda, the one that just doesn't seem to make sense from a, we are pretending to have a massive space battle, sense is the way ships activate. Why would the fact that there are two more CR-90's half way across the battlefield make it harder for my ISD to chase down this Corvette right in front of it. From a narative sense it doesn't make much sense.
But it does from a game play sense. I lets little, far less powerful, ships compete against big nasties like ISDs. The "Game" part of the game works. And if the buying a couple (or more) flotillas lets me have an ISD and have 5 activations, then they are a hugely welcome part of the game for me. (Since I love ISDs, they are the reason I play this game).
So for the record, I don't think Flotillas, or any of the things they can do are overpowered. It's not something only one faction can do, and it doesn' push other ships out of the game. In fact, I think they make ISDs more playable. The problem is a disconnect between what is good for the "game" and what seems like it should be good for the imaginary battle that takes place in our heads. And in all comes down to how activations work in this game.