Originally I thought 40k fluff was base and unimaginative with words like melta, plasteel, and things of that nature. Seemed lazy.
That Iron Snakes novel, Brothers of the Snake or whatever, was what got me into 40k fluff. And 40k fluff has always irritated me but I like the overall feel of the galaxy.
Yes from a logical standpoint the Chaos Gods should win in the end but I've tried to think about 40k as if it were 30k and we didn't know anything that happened up until 40k. At that time the Emperor had restored Mankind to dominance, he had 20 demi-gods (while basically being a god himself) leading legions of super-humans on an all out slaughter of anything not-human.
They crushed every alien before them from ork to elder. Chaos corrupted cultures (while not overt as we know them in 40k) we just as easily crushed. If we played Warhammer 30k at the height of the Great Crusade (well before the Heresy) we'd probably think the Emperor was going to win, all things considered. I still hold out hope that if the plot is advanced something else will happen, where the victor isn't as clear as we think it might be.
Sadly from what I understand the plot isn't going to advance for 40k like in Fantasy. Which, given the rumors I've heard and if this "bubble theory" has any credence, I'm actually glad. Fantasy was always the weaker setting better for it to be experimented upon than 40k.