Good points, both of you. I was going for that they MUST Deep-strike; half (rounding up) shall come out of Reserves by means of Deep-Striking while the rest will come via preceding turns ala rolling whether they come of Reserves if they make the rolls. Like Deathwing Assault but we be calling it Grey Knight Assault. I dunno it is acceptable to give Grey Knights Drop Pod or Rhinos. There's so little fluff on such deployment and their delivery system. That's why I thought make them all Deep-strike as per their specialty that I have read so far in their fluff. As for the FA PAGK, wanna give them Jump Pack + Heroic Intervention? 
Just an idea; you may tear it up and throw it away.
I am loathe to give Grey Knights a rule akin to DP/D/D Assault, simply because those three armies already get it. Yes it fits, and reduces the waiting and randomness, but it's replicating rules already found in Marine codexes (for two out of three, at least). I do have an idea on the matter, though, but I will go into more detail on that further on.
Do NOT give Grey Knights Drop Pods or Rhinos. Just don't. I have an idea to improve their mobility, but I'll detail that later on. And definitely don't give them Jump Packs.
To be honest, I dislike the idea of PAGK; my idea of Grey Knights comes from 2nd Edition where all you had were Terminators and they were absolutely rock hard. However, I am willing to accept that PAGK are currently available and to create a new codex without them would annoy an awful lot of players. Ergo, PAGK have to stay.
Giving them Frag Grenades would just make things sooooooooooooo much easier IMHO. The Krak Grenades as for those Grey Knights that eschew their Nemesis Force Weapons and Storm Bolter for Special/Heavy Weapons.
I can't deny that giving them Frags makes things so much easier, but we've seen an instance of where a model has an ability that grants the unit the equivalent; Eldar Harlequin Shadowseers have Hallucinogen Grenades that grant the unit Plasma Grenades. Therefore, there's no reason you couldn't give the Grey Knights an 'equivalent of Frags' ability or psychic power, like I suggested previously.
The other thing is that I like the idea of Grey Knights being so badass that they don't need the mundane equipment that 'regular' Space Marines use (even if they replicate the ability with a psychic power). This goes especially for Krak Grenades; you have a weapon that grants you the ability to destroy a Dreadnought in melee, so if you choose to give it up to tote a better ranged weapon then it's your own fault for doing so. Giving PAGK Krak Grenades makes taking Special weapons a no-brainer choice, since you still get the Strength against vehicles.
I've decided to redo the entire "We're good against Daemons so we have these Special Rules..." Special Rules. Trying to go by RAW; these Special Rules should affect anything from the Chaos Space Marine and Chaos Daemon Codices. I thought I make them "almost free" since the Special Rules itself can only affect a narrow margin of the 40K armies but I feel we're going to need to discuss this extensively.
The thing is that Daemonhunters, or Grey Knights at least, should only be fielded against Daemons. There is no real reason why Grey Knights should face something non-Daemonic (unless it's because it's in the same army as the Daemonic enemy but in the way). Personally, I would like to see the Adversaries section become compulsory, but the enemy's Daemons be free of charge and models provided by the Daemonhunter player (assuming the other player doesn't have his own models he wants to use). That way you will ONLY see Grey Knights when the enemy has Daemons, which is pretty much as it is given in the background.
With that in mind, I would suggest that the rule akin to "Grey Knight Assault" basically mean that Grey Knights held in reserve may not enter play until any enemy Daemons do, but at that point they AUTOMATICALLY enter play (or give them a staggered, yet non-random, deployment like in Apocalypse; up to half may come on the turn after the Daemons enter play and the rest must come on the turn after that). Since the enemy always has Daemons, the Grey Knight player will always enter play at a reasonable time.
For mobility, I would like to see the ability to be removed from play and teleported across the battlefield. Grey Knights are known for their Teleportation prowess and I think that would be an interesting way to improve their mobility without giving them Transports. Whether we do this in a similar manner to the Eldar Skyleap (removed from play and put back into Reserve) or the Necron Veil of Darkness (instantly redeploy via Deep Strike) would need to be discussed.
I don't think its a silly matter. On the contrary, it's a serious matter especially when it comes to RAW. Aye, I want it be as RAW-friendly as possible while being RAI-friendly as well. I will first read through the profile for the Searchlight, Acute Senses/Night Vision USR as well as Blacksun Filter to see how they work first before I write up the rules for Shrouding. Honestly, I don't think those things work especially when it's a de-facto Psychic-base defense. Again, another matter to discuss extensively.
To be honest, Shrouding, as it currently exists in the background, should NOT be affected by any of the aforementioned abilities or wargear. It is somewhat akin to the Eldar Shadowseer's Veil of Tears (though far less effective).
Perhaps you could allow any Psyker, or unit with a Psyker attached to it, to reroll the result for Shrouding (representing the Psyker in a battle of wills with the Grey Knights to pinpoint their position)? That way it's a similar situation for Night Fighting in so much as almost every army has something to help them in that manner, even if it's not the same thing to help them out for both.
True; maybe a Venerable Dreadnought and "normal" Dreadnought for the Elite slot while we have a Mortis-like (IIRC it's the Dark Angels double Twin-Linked Autocannon-armed Dreadnought) Dreadnought for the Heavy Slot. Yet, another matter to discuss.
I'm fully aware of the Mortis Dreadnought. To be honest, though, it's a case of what Daemonhunter players have done with Dreadnoughts on the tabletop more than what their background suggests, as they're the only real long-range shooting, in particular anti-tank, that a pure Grey Knight army can include. There is little given background for Grey Knight Dreadnoughts and I cannot see any real reason why they should favour one over the other (shooting vs. melee, I mean).
If anything, I would suggest that Grey Knight Dreadnoughts, in a similar manner to how a regular Grey Knight has a Storm Bolter and Nemesis Force Weapon, should be forced to wield a DCCW and a ranged weapon, as this gives them a thematic tie in with their smaller brethren. At that point, however, the question of where to situate them in the FOC is still open for debate.
The other thing to bear in mind is that would a Venerable Grey Knight Dreadnought have WS 6?
Anyway, I've thought over it for awhile and chills me to the bone if we were to use the current IG's Storm Trooper to be placed as Inquisitional Storm Troopers. That makes our Troop Choices 20+ point each. We're going need a cheap troop choice.
I agree. There is no way you can include the current IG Stormtroopers as Troops. As they stand, the current Stormtrooper entry is fine, though I would consider dropping the points costs by up to 2 per model, including Frags and Kraks as standard (with no option to upgrade to Melta Bombs except for the Veteran), and forcing you to take 10 models to get a second Special Weapon. I would also consider renaming them so there is no confusion between an Imperial Guard Stormtrooper and an Inquisitional "something", even if you continue to use the same models.
There's also that matter of Assassins, none of the 5th Edition Codex I've seen put limitations on any unit. I can't imagine playing 3 Assassins will get me friends. So, I thought Assassins don't take up any slot but the player must take an Inquisitor Lord for every Assassin. What do you think on the matter?
Assassins need fixing on so many levels it's tempting to just remove them from the Codex completely. I do like your idea of "one per Inquisitor Lord", in a similar way to Imperial Guard Advisers (but obviously detached from the retinue). In fact... you could even make Death Cultists Retinue members, so rather than being a poor-man's Eversor they could be used to give Inquisitors more of a bite in melee (something sorely needed right now, IMHO).
As for the temple assassins, they would need a major overhaul in terms of rules. Not sure how to do that without them being too overpowered, but the removal of Allies rules will help a lot (as suddenly they don't become available to all and sundry within the Imperium, and thus capable of teaming up with the worst parts of the other Imperial army lists). I also think that unique stat-lines for each of the assassin types would help distinguish between them (such as BS 8-10 for the Vindicare).
