ED Ship Yard
^ That's the current loadout I run on my "Vette after a metric tonne of testing. The 2 cannons have autoloader, the 1xLarge 2xMed MCs have Incend Rounds, the 1xSmall MC has corrosive and the frag cannon has drag munitions. It obliterates...everything. Huge autoloading cannons do filthy amounts of DPS, almost as much as PAs against engineered shields, more against unengineered and leave PAs in the dust for hull damage (punching out an elite-conda's power plant in a single salvo is sooo satisfying). Although incend rounds increase heat generation by 200%, a large and 2 smalls don't budge my meter, even with a G3OC power plant. The thermal damage is much nicer for tearing down shields, not sure what Jankula means about the disadvantages against hull as kinetic is +20 vs hull, -40% against shields, while thermal is +20% against shields, no malus or bonus vs hull, making them a nice addition to the kinetic damage of the cannons. You're giving up a little hull damage for a tonne more shield damage, which is where a kinetic loadout falls short. Then again, I haven't tried all autoloader MCs, so take that with a grain of salt.
I used to run 2 small feedback rails for SCBs on the bigger craft, but since I couldn't lead the cannons while using them, and SCBs on anything other than Elite ranks is trivial, I swapped them out for the corrosive buff on a small (freeing up my large MC for inced rounds) and a drag cannon. I was spectical of the drag cannon's usefulness at first, but I'm glad I tried it, it's amazing for keeping FDLs and FGSs and even Vultures in your sights, couldn't go back to not having one now.
Run whatever loadout makes you happy, but before you engineer everything, keep in mind that MCs have surpisingly limited ammo, and different hardpoint sizes fire at different rates. I originally tried a full MC loadout and got tired of the redock/synth spamming every 30-40 minutes, and my smalls running out 5 minutes before my meds, which were dry 5 minutes before my large etc; felt like I spent more time keeping track of all my different ammo levels than looking for new targets.
Edit: Firing groups can get a bit tricky with the above. I have the 2 cannons + the gimballed drag cannon bound to my secondary fire (drag last the 4-5secs until I fire the cannons again, so works out well) while the 2xmed 1xLarge MCs are bound to primary, once the shields go down, I switch to my second firing group which adds the small corrosive to my primary fire. Just don't let your crew fly it, they'll spam everything and you'll be out of drag/corrosive in 5 minutes.