I don't see any reason why shields should simply be nullified in Lockdown. The shield-button does class-specific stuff, so what? Can't it still shield?
The effect of using a custom shield as a guardian should be pretty obvious, (just stack the shield's bonuses on top of the guardian shield's bonuses, the guardian shield could use a slight buff anyway), but what about strikers and recons? It's simple; add the shield's stats to the player's defences whenever the ability is used.
A recon getting hit while cloaked would therefore take less damage than when he's not, but if he's hit while cloaked he loses the cloak anyway. More importantly, it means a recon with a status-resisting shield can walk through appropriate haze bombs. The resist would disappear the moment he reveals himself, but the option is there. I play a guardian bomber in LD, and personally I'd love to be killed by a recon for a change.
Same thing with strikers: add the shield's defences exactly when the striker is dashing. Again this would allow the striker to dash through appropriate haze bombs (but I'm predicting most skolver clones will just get a swiftstrike buckler anyway, which is fine).
And then there's the other suggestion. A lot of the armour lines are themed after enemies. Why not let enemy damage bonuses apply to these? Damage vs beasts would apply to wolver coats and dragon armours, jelly bonuses against the jelly mails, undead versus the skelly suits, gremlin bonus against the bomber armours, fiend versus the angelic sets, and construct versus the plate sets. It'd go a long way to making these UVs and armours with these bonuses less useless.
Not sure about how adding a second shield slot of sorts would work. I think the devs just stuck the class mods in shields because it was a slot that everyone has, and not part of a set of any armour.
However, marking knights by the armour they wear is rather stupid. Skolver is wolver, and wolvers are weak to pierce. But skolver defends against pierce. And how are bombers classified gremlins? They could be demo knights, weak to elemental instead of resistant. How are the plate sets constructs, because they are made of metal? And what if someone mixed armours? Would they then be weak to both types of damage?
Another problem is that most armour sets with damage vs family are in fact, based off a family themselves. So by using a chroma set, you open yourself up to more pierce damage.