I have no problem running with a gunner on my ships. The idea that a gunner is useless is unfounded. However, I do think gunners could be buffed a bit. Engis just have too much utility that you give up when you go gunner, and I don't think gunners get enough of a damage boost over engis to compensate for the loss of utility.
Now, all of this depends greatly on the load out of the ship, the ability of the crew and pilot, and what the other ship(s) you are running with is doing. But on the whole, I think gungineers come out ahead of the gunner, but it isn't like the gunners are useless or a detriment.