...Also, like I said, any big ship currently can be completely owned by a couple of counter-fitted dirt-cheap ships. Or one even if the pilot is really good. You can't go more vulnerable than that. And this is not ok in my book. This is like bringing down a tank with a handgun.
Several people working together with ships specifically tailored to the situation taking down a single player in a big ship that
isn't prepared for the situation? Honestly that sounds fine to me. While a single small ship can kill a big ship, there needs to be a large skill disparity, the small ship needs to not make mistakes, and the big ship needs allow themselves to die. I've been able to take down the shields of big ships in my mine-bomber Viper IV, but the only ones I've been able to kill are the ones that don't pay attention to their module health, and allow me to kill them. If a ship has a few PDTs, it makes it extremely hard to hit them with the mines. If they have a few ECM, it makes them extremely hard to hit with torpedoes. If they fly smartly, it makes them extremely hard to hit with either. Even if they fail to do any of those things, they could at any time simply go to supercruise and there'd be nothing I could do to stop them.
Using a little ship to kill a big ship (NPCs and their poor, non-engineered builds aside) is
not an easy thing to do, even if you have a bit of a skill edge on your opponent. Just like killing a battleship with a lone destroyer is possible, but not easy- a lot of things need to go just right for it to happen. I would personally find it very lame and boring if big ships were just invulnerable to little ships. Flying a big ship would be a total bore vs. most targets you encounter, and flying a little ship would be too cut-and-dry: see a big ship? Just run. You can't scratch it.
You can't "swat them like a fly" in any big ship. With the new dirty drives engineering any small/medium ship is one boost away from getting to safety. There's absolutely no way to get them (unless the ship is fitted very poorly or the pilot just doesn't care or wants to fight to the end).
You can DD mod the drives of the big ship, too, so this point is kind of moot. All engineering is available to all ship sizes.