EDIT - I don't know if this is a bug, but you can currently swap out your two ship slots and release more ships than I believe you are supposed to be able to. I assume the ships you had in those slots are supposed to come back in to your ship, and they don't right now. This is why people are seeing huge balls of ships around cruisers, everyone is abusing it.
So far playing with the carrier has been anything but enjoyable. I really wanted to play the cruiser, but without useful rank 4 abilities, there's just no point. Of course not having a ship flying skill hurts as well.
The carrier is beast, no doubt about that, but there's no way the thing is overpowered. I'd rather not even have it, and I'm sure that after most players take a shot at trying to fly it, they will realize that as well.
I'll point out the main reasons here in no particular order.
Too many skills. This ship acts as science so you get all the targetting subsystem skills. This means that you're easily using all 3 rows of skills. Even with multiple extra mouse buttons the thing is pushing 'too complicated.'
No turning/icing - The thing flies horribly. When I come out of impulse and turn all my power on reverse, the ship still skids over 5km before I can even get it to come to close to stopping. And turning? It appears to CAP out, yes CAP OUT, at 9.6 turning rate. Additional thrusters seem to cap there for the ship, and the 30% turn rate increase appears to do nothing. I don't know how a 30% increase could not be noticable, but it's not.
No Cloaking - Perhaps the biggest point, this ship is a huge liability in PvP unless there's a full team. It can't escape due to it's massive side and thus slow speed/turning and it can't cloak. MES doesn't work so you can't replace it with that.
I don't see a lot of players giving up the alternative counterparts once the Negh'var gets fixed.