A couple reasons: I'm only allowed 5 options for a poll and Grey Knights, while cool, aren't as popular as the Black Templars (on the forums at least); nor are the Grey Knights a First Founding Chapter. Also, like Aquinas said there is little to no chance of them being playable at launch.
I've suggested that they consider allowing Successor Chapters of the main Chapters be playable. So Ultramarines can play Iron Snakes, Mortifactors, Praetors of Orpheus, etc.; Dark Angels can play Angels of Vengeance, etc. Effectively, have 5 Chapters mechanics-wise, but allow some custom variety with the option of picking a Successor Chapter as part of it. If that were the case, then you could have both Black Templars and Imperial Fists, since Black Templars are an Imperial Fists Successor Chapter.
While I think it's always good to have options, if successor chapters are aloud for each 'main chapter', you're going to have 10 or so chapters running around. Now it might just be my personal preference but I'm don't like the sound of that. From a lore stand point, it bugs the hell out of me for one. Why are 10 chapters fighting on the same planet? Seems a little ridiculous at least. And then we have the rainbow colored battlefields with squads made up of 5 different chapters. It sounds messy to me. But maybe I'm sticking to lore too much... Just my view.
A crusade is the perfect excuse to involve many chapters. I see no argument against this! It is the will of the Ordos and my edict that we include as many chapters as possible.
Maybe if there are more planets added to the game in the future. For example, there are 5 chapters fighting on one planet, 5 on another, etc. etc. In this way we could avoid the, "Every chapter is fighting on this one planet!" problem where every chapter is underrepresented because there are so many. I would find that to be ridiculous.
