I was always on the 'kinetics/anti-shield are better' bandwagon, but I've been mounting a lot more anti-armor and anti-hull lately and been getting even better results.
It might mean that I just don't have enough strike missiles, but when I go heavy kinetic the enemy just doesn't die fast enough. With more HE and/or high dps hull crackers, it takes a bit longer to push the enemy flux up but the kill is so much faster. If I'm going through the work of fluxing out an enemy, I want to do some real damage on top.
This could also be a result of me almost always going heavy combat skills: I can safely sacrifice some weapons that would help the 'flux duel' because only a very very rare enemy officer, in a unusually well equipped ship, could possibly win a flux duel with my own ship. And also the fact that as often as possible I'm attacking vulnerable ships that are under fire from my allies (and the same goes for my allies, I order them to gang up on lone targets). If the ship is already high on flux kinetic weapons are a bit of a waste.
For example, my current Eagle loadout is: 2x heavy autocannon, 1x heavy mortar, 2x phase lance, 1x ion beam, 3x lrpd, 2x pd, ITU, IPDAI, Hard Shields, and turret gyros. A few months ago I would absolutely go 3x HAC, but I'm simply getting better results with the heavy mortar in there in real combat.