I have to do the weapon swap animation anyway, that's enough of a time cost for doing it. To have my freaking grenade and focus go on their full CD every time is just spitting in my face.

I've taken to evaluating weapons not by their value for a job, but by 'Can this kill flesh and armor?' because swapping isn't really an option. Enemy in melee range? Back up or take it on the chin, because pulling out even a Chainsword will take too long.

This has put me in the weird position of basically using the Bolter for everything, since it's got armor break on two attacks and fleshbane (AoE on top of that!) on another. Initially I tried to match Autogun and Plasma, but swapping just started to annoy me for the grenade/focus CD effect, not to mention the only anti-armor moves on Plasma rifle have a notable CD.

I don't think it's healthy to have this setup long term.

Since the weapon swap cooldown change. I only use 1 weapon set. There just doesn't feel like much of a reason to have the second set at all now.

I agree that swapping the weapon should not instantly set the cooldown of grenades, armor skill and weapons skill 1&2 to zero.

But triggering the cooldowns every time you swap a weapon is also not a good idea. 

Currently the weapons are very unballanced, and close quarter weapons + meele weapons are very weak compared to ranged  weapons like Lasgun/Bolter or Gravigun.

But later in the developement phase, where swapping from a long range weapon to a close ranged one will be a strategically important option, having the cooldown triggered will only elimminate the need for weapon swap.

Yeah, exactly.
Now even special ability have cooldown after You swap weapons, that's really annoying.