The problem I see with the Trojan War scenario is twofold, a) it's a bit of a simplistic way of using the 'marine = Greek Hero' of Ross's similie, which is admittedly a not terrible way of looking at marines, and b) it is very much just a warry campaign, a string of pc combats tied together with the occasional argument between protagonists, there's not much in the way of problems to solve with anything other than your pc's bolters and chainswords.

I think there are better ways to play space marines.

For example - a campaign on a single ex-Imperial planet riven by barbarism and factional conflict for millenia, where the pc's are sent to scout the world, and if possible set about returning the world to compliance. During the course of the campaign the pc's must decide which of the world's 4 nations is closest to Imperial orthodoxy (if any) and to favour. This would require talking to npcs, weighing their cultures, trying to learn if any Chaosy type stuff is going on behind the scenes, perhaps getting into the deeper mystery of why the world fell into anarchy 2000 years ago, as well as helping the people the pc's decide are 'the good guys' against their enemies.

THE BATTLE OF TROYOUS

A small moon that was a former Maiden World has been overrun by the Eldar. They are bunkered down in a ancient and massive city protected by an impenetrable power field of arcane origins and gaurded by a massive eldar army led by a Farseer and his personl champion, an Autarch code-named 'Hektor' by the Imperial forces. The Imperial Army is led by General Agamemnon, an old foe of the Farseer, who is determined to end their decades long conflict here and now or die trying. The players are a DW kill team nicknamed 'The Myrmidons' led by Captain Achilles.

All the high points of the Fall of Troy could be included as small scenarios, including boastful challenges between Exarchs and Marines leading to one on one combats and sneaky attempts to take the city by stealth.

Adam France said:

Why would Deathwatch, or for that matter Ordo Xenos, be involved in such an affair? 

Atheosis said:

I could think of several possible reasons, off the top of my head; there's some form of xeno activity on the planet, perhaps the planet has xeno ruins on it that are in some mysterious way central to the uber-plot, perhaps a xeno race or cult is offering favours and possible alliance to the various planetary level factions and there is a question as to why?

EDIT - On a side note, I do think though a clever way of bringing together marines from different Chapters, there are also problems with the DW being the assumed unit. It does kinda require a xeno aspect to every mission. Okay, other things (such as Chaos or whatever) could crop up as a surprise and need to be dealt with by the pcs, but I do think it's a potential limitation using the Deathwatch. I'd be tempted to have the pcs as members of a single Chapter personally to avoid it.