Well, I'm going to swim against the tide to say that I really like where this is going. I think there is a space for players that want to play highly upgraded versions of standard ships. Adeptus Mechanicus should have done this, but the randomness in the list is a huge turnoff for players that like to tinker.
Some suggestions:
The Black Ship - I like the general direction; heavily protected but undergunned. However, I think the Black Ship should be more carrier and lance based than it currently is. Remember that the weapons systems are there purely to protect the ship, and AC have a defensive, as well as offensive, role to play. I also doubt that the Inquisiton would rely on standard transports to uplift their precious, psychic cargo, so perhaps resilient Thunderhawks would be a fit?
Because the Black Ship is going to want to escape pursuers (such as the torpedo escorts that destroyed the planet killer) it is not going to want to have to maneuver (always bad for a battle ship) to bring it's guns to bear. So a strong dorsal lance array would be fitting; the hangars could be on the side of the vessel, much like on the Emperor.
Any reason why it is not 6+ armour? I'm also not sold on the torpedos - what would it need torpedos for?
This ship has potential, but it currently feels confused, and I'm not clear what it would actually do in a game of BFG. Being able to soak fire is great, but I just don't see my opponent's bothering to shoot at it right now.
Grand Inquisitorial Cruiser - I like the concept very much, but why have you used cruiser base stats rather than grand cruiser base stats (given the name)? I see this more as a center piece rather than as a line ship, so perhaps it could use a few more side-grade options, to reflect the individualistic nature of Inquisitors? Alternatively, perhaps just drop the "grand"?
Grey Knight SC - A nice touch.
Inquisitor Ordos - I like the direction, but not the execution. First, if you feel something is too powerful, then up the points cost. Don't make games (or tournaments) complicated by modifying your opponent's fleet list. Second, kill the random factor. Randomness is a huge part of why the AM fleetlist was such a disappointment. Rolling for upgrades kills strategy and tactics.
-Silent Requiem
