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Can I use both groups freely between one another?
Now that I've got the big question out of the way please let me elaborate. I have been an avid painter (casual player) of the 40k series and have only recently begun playing the game. I chose Grey Knights as my army since I ended up buying more of their units than any other and got absolutely crushed in my first game (I suppose that's the entry fee, huh? ). Since my devastating defeat at the hand of the Eldar I bought my newest Gey Knight codex and picked up the Astra Militarium one as well because there are a lot of their tanks and aircraft I enjoy painting. After reading through the codex's I found that all imperium forces can be played together on the field. Is this correct or am i interpreting this wrong? Once I read this I immediately went to the store and bought a Hydra and a Valkyrie gunship. I quickly assembled and meticulously painted the two of them over two weeks time. they came out wonderful in my eyes. So, when I propositioned the person who beat me last time to play again he agreed. As soon as I started laying my 1500 point army (may have been more) onto the table I was interrupted and told that he would not play me unless I had at least two squads of Grey Knights (not including my Paladins), and another squad of Imperial Guard. I was awestruck. I just stood there as if wanting to say, "But I want to use armor with only a few troops. this is my army, not yours". So, I had a few words to exchange with him and I eventually packed up my things and left. Was I warranted in my thinking? Can I not having Imp Guard Armors/Fliers with Grey Knights?

My Grey Knight army is as follows (complete loadout excluded to expidite):
Castellan Crowe
Lord Khaldor Drago
Grey Knight Paladins
Grey Knight Terminators
Grey Knight Venerable Dreadnought (Power Fist and Twin Linked Las Cannon)
Imperial Guard Valkyrie (Hellstrike Missiles and repeating Laser)
Imperial Guard Hydra (Twin Linked Flak Cannons)
*Optional* Grey Knight Land Raider (Twin Linked Las Cannons)

Any ideas what I've done wrong or why I was given that response to my army?
*edited due to error and such.

Your opponent did not want to play against an Unbound list. People dread unbound because you can make broken lists. In my inexperienced opinion (regarding GK) that army doesn't look OP.

While I myself have nothing wrong with Unbound lists, it would be good sportsmanship to make sure your opponent is okay with fighting one.

As for your list itself, it's perfectly fine. I don't see anything at all OP about it, and I think the theme is just fine.

You should look up the difference between a battle forged army and an unbound army. What you have there is an Unbound one and a lot of people don't like those. But you can still play both grey knights and astra militarum in a battle forged list you just need to meet some list building requirements (which is more or less what you opponent was referring to).

Ah, ok. It just felt like the guy was turning his nose up at me as if my army wasn't good enough to play against. After a bit of digging it would seem that I need an HQ and a troop choice for the Astra Militarum forces and I should be good to go. I'm thinking Commissar Yarrick and Veterans. Good idea or no? Is there a better HQ choice?

You'll probably get better advice in the Tactics forum, but I think Veterans are generally considered to be a good choice. I feel like most people get a Company command Squad as the HQ, but I may be wrong. The Tank Commander might also do well for you as it's basically 2 Leman Russ tanks that take up an HQ slot.