in the current version is that:
Spoiler
The Valken III has upgrade paths and flexibility that the Valkazard simply lacks, especially in the late-game when you have a lot more Super Alabaster tech available to you. This is probably going to become more prominent in .98, since we are definitely getting a firmer, more fleshed out endgame in the upcoming patch. You can also use the build-in system to largely restore all of the 'Zard's tricks onto the III, if you really want to, thanks mostly to the drug system being its own rare salvage-findable modspec.
The Valken III is also a lot more practical than the 'Zard, especially as of the current version. The Valkazard feels great early on, and will let you do stuff a ship that size should struggle to do, but it's really over-costed for what it is and it's going to feel like more and more of a drag on your fleet (and even your ability to level up!) the further into the game you go.
So it really becomes a question of when you want to give the 'Zard up, and how long you potentially want to wait to get a III. It can take a little while, especially if your rep with Sera is low at the time of handover, but in the long term the Valken III is the better machine to use, I think.