On the FS Yahoo mailing list, someone asked about the difference between 40K and FS. It's an interesting question; I've posted, but I'll stick it up here as well so it doesn't let lost in the noise.
For me, the difference is simple; subtlety and space to ask questions.
40K has EVERYTHING turned up to 11; one hive city holds the worlds' current population, a Super Star Destroyer would only make it as a frigate and everything is nastier than everything else. I mean, just look at the bad guys; zombie robots that serve soul-eating star gods, god-level manifestations of raw human urges, fungal super-soldiers that not only fight but infest so there's a never-ending source and some hive-mind god intelligence eating our galaxy and turning our own biospheres against us.
And all of these are fought by demi-human supersoldiers with guns that fire rounds bigger than your thumb.
The morality is black-on-black; the good guy is a fascist, xenophobic human empire that uses criminals as spare parts and got its fashion tips from the wrong side of WWII.
And the thing is, all of the technophobia is good and necessary after the scrap with the Iron Men. Psykers need to end up as the God-Emperor's lunch because that's what keep space travel going and because until they mature they'll only serve to break reality. You can't stop and ask if it's OK to bomb a planet of civilians because you'd already be eaten by whatever got to them.
And that's awesome (I should point out that I have both DH and RT and I think they're great). Everything is supposed to be epic and more than a little mad and hardcore - the political conceit of being hard men making hard decisions made very real, desperately fighting to survive just one. More. Day. Against things that would make Cthulhu go 'I'm outta here; this stuff is *whacked*'.
Compare with FS; each of the sects has factions ranging from evil bastards to moral paragons and most shades in between; even the symbiots as written are a weird transhuman thing that doesn't quite work out, rather than the 'consume!' thing of the Tyranids.
Yes there's technophobia and space feudalism too, but they're inverted by being painted as a choice. The nobility took their chance when the Second Republic fell down, and remade the Known Worlds as they wanted them - and they had to fight to do it. The Guilds' precursors built the Second Republic and would like to do it again in some form.
In many ways it's classic sci-fi of the type we don't see often enough, questioning the human condition.
Tl:dr: Fading Suns asks 'why' - why did all this change and can we escape it? 40K says 'blessed is the mind too small for doubt. Now reload and let's get that thing or die trying!'