Hi,
ah, a setting for a cool discussion.

Do you really think the FW list is all that powerfull? In battles under 1000pts the list is pretty okay, but once you go over 1250pts the GW Tau fleet is much stronger! Yes, GW Tau won adepticon 2008-2009. If you want do something about strong things the GW list is to fix first.
The Protector as stands is a capable vessel, better then Lunar on attack (what you pay for +10pts) but less then the Hero. The Hero wins against both. So there logic fails, as said, background said weaker ship, stats make it better. Restrictions to size down problems is not a good solution. The Hero should drop weaponry all around.
The FW list isn't as over-powered as you say. I have won with them numerous times but I have also beaten them. They are on the fragile side. The Explorer is a better carrier then the FW Custodian. Now, this new Custodian by the HA is better then the Explorer for what it needs to do. Going from 2 to 3 shields, adding Tracking Systems. You give it 45cm Ion Cannon.
On the prow deflector: it are shields that are formed that way, not the hull. So a prow deflector could be mounted on any vessel. But, alas, with all improvements giving no deflector won't matter tbh because you just created a beast.

I think, as it stands with powerfull, the FW list is fine. Not too strong, not to weak. A fleet like Imperial Navy & Chaos. Fine with me. It needs some finesse to play with.
The GW list, harder to learn, but in the end much better in larger battles. A list already capable of running down Necrons!
GothiComp = running paiting competition and one entry is called a Commerce Citadel vessel, first time I heard it and now it is in a list. Coincedence. Funny.
Playtesting : the FW list is used by everyone around and has seen many playtesting by now as far as I see. The main complain is that the Emissary is useless. Everyone screams 90* at least. It is a sitting duck and easy victory points to any opponent.
And the Emissary cannot kill a Marine cruiser as it stands, even with 90*. The whole fleet par Custodian should be 90*

The fleet list: if you keep this list, which means, limited Protectors, everyones FW fleet will become a fail. Everyone has more Protectors then Emissaries and now this list means you need more Emissaries. You are urging players to spend money. I do not have that money for example.

So that is a NEEDED fix.
cheers!