4 flagships? Sounds like he encountered Uomoz's fleet. I can't actually help much there since I haven't actually fought Uomoz's boss fleet yet, but basically, for bosses overall, you want to be able to innovate. My boss fleet, for example, is meant to destroy anybody who is using the slow and stompy ships that a lot of end-game people use, but is completely vulnerable to swarms of smaller ships because of the way its weapons work. The thule meteor and hadron accelerator can destroy just about any one ship in a single or couple shots, but you can still win if all it destroys with that shot is one frigate out of 20. Uomoz's fleet is just about the opposite of this, from what I can tell. It uses several big stompy ships that can overpower any regular fleet, but I bet it could easily be taken out with some carriers and'a half dozen organized strike wings, or perhaps a player-controlled capital ship with all of those flagship specific boosts (which none of the boss fleets have)
Basically, the boss fleets are supposed to challenge end-game people with a fight that they can't just win with any fleet. The biggest boss fleets make sure to be larger, so that the player has to innovate and try new things to win. They are not meant to be fair, they are meant to give a challenge players who are no longer challenged by fair fleets.
As for the boss fleets ruining the game, I simply have to say that no, they do not, because you do not have to fight them. You can ignore them for all of eternity if you want to, and by ignoring them they ruin nothing. I believe that their presence in the mod to challenge those who want a challenge, however, is a boon to those who like such challenges.