Alright here's proposal #2 with your input in mind!
Recommended Revisions:
Ld 9 Inquisitor 50pts
Ld10 Inquisitor Lord 100pts
-Inquisitor Lords belong to an Ordo. Choose one of the three Ordos that the Inquisitor Lord belongs to an apply the special rules that Ordo provides.
Blackship
-Blackship should not award renown for surviving because that only gives you the reward in campaigns. This should reward VPs if it survives. If it dies, the killer gets an extra 200vps. If the Blackship survives uncrippled and not disengaged, it give the Inquisitor player 200vps.
Grey Knight Battle Barge needs its own page (I have already created it)
Inquisitorial Cruiser (now 270 pts with the following rules)
-1 Inquisitorial Cruiser pre 3 cruisers. Takes the spot of a Grand Cruiser for fleets that use Grand Cruisers.
Ordo Heretius
-+2 to boarding, +1 to H&Rs and -1 to H&Rs against them
-Canoness Superior (function as Secondary Commanders like in the IN fleet)
-Sisters of Battle give the ship +1 to Boarding. +5 pts
-Inquisitorial Storm Troopers (function as Honor Guard without the SM +1) which may be taken on any ship with an Inquisitor or Canoness Superior. +5pts.
-Any Battleship or Inquisitorial Cruiser with an Ordo Hereticus Inquisitor Lord on it is considered to be an Exterminator ship or is given the Transport quality, depending on the relevant scenario.
The promary advantage of the Hereticus is in the Sisters of Battle boarding bonus that can be taken, which will make them more powerful in boarding but not too much. Also, the bonus Exterminator or Transport upgrade is the other. This adds to the feel of Hereticus which is all about cleansing Humanity and ultimately needs to invade and often Exterminatus worlds to have this done. The Exterminator upgrade is so... Inquisition...
Ordo Malleus
-+2 to boarding, +1 to H&Rs and -1 to H&Rs against them
-Brother-Captain (function as Secondary Commanders like in the IN fleet)
-Grey Knight Purifiers (function as SM Honor Guard) on any ship with a Brother-Captain or an Inquisitor on it.
-Grey Knight Paladins (function as SM Terminators) on any ship with an Inquisitor Lord on it.
-Ordo Malleus ships are immune to the effects of Marks of Chaos and Daemonships.
-A ship led by an Ordo Malleus Inquisitor Lord may take 0-1 Grey Knights Battle Barge and Grey Knights Strike Cruisers instead of regular Strike Cruisers.
Malleus can take Terminators. That's a difference from the Hereticus. Also, this unlocks the Grey Knights options and provides the nice little defences against Chaos.
Ordo Xenos
-+2 to boarding, +1 to H&Rs and -1 to H&Rs against them
-Watch Captain (secondary commander exactly like they are in the IN list)
-Deathwatch Kill-team (counts as Honor Guard) may be taken on any capital ship. Ships with Kill-teams always get a +1 to H&Rs caused by their vessel and vessel's ordnance, even when not attacking from an Inquisitor Lord's vessel. +15pts
-Deathwatch First Company (counts as Terminators) may be taken on any vessel with an Inquisitor Lord.
Xenos looks much like Malleus but cannot get the goodies of the Grey Knight fleet. Instead, it gets the Deathwatch Kill-teams upgrade option.
Refits - leave the refits to the Adeptus Mechanicus. Giving Inquisitors the ability to take refits isn't a good idea considering you can put an Inquisitor on an Admech battleship. I have changed my mind on this. Also, it keeps things simple to not have them
*The last page in the 2010 Inquisition document can be simplified greatly into quick bullet points. It doesn't need to be so dang big and bloated.
*No more general "Inquisition Strike Cruiser" because it makes sense that Deathwatch wouldn't make a fleet out of them.
*The Ordos have been cleaned up a bit to look a little more like a Space Marine upgrade and allow for more options to be taken relating to that Ordo. Each Ordo has some advantage over the other as referenced above.
*There will need to be a rule that says that Inquisitor Lord boarding an H&R upgrades do not stack with Space Marine special rules.