I'd say that what makes the AFMkII better is the ability to take ECMs. Straight up. There is nothing that can one-shot an AF with ECM, possibly even with a double arc, but the Pelta can easily be one-shot by plenty of suped up ships.
What makes the Pelta awesome is the ability to take 2 officer upgrades with the title. You get so much utility out of that, combined with the fleet support upgrades.
Edit: take that back. The Avenger could potentially one-shot an AF, but that requires very precise setup.
Edited by Parkdaddy