If you were Captain Ret-Con for a day...

[marsdonut]

I would only cut down on all the fluff to weapon talk in the codices, to reduce on the non-rule clutter. They would be available in another section of the each book with sample chapters, short stories, xeno-perspective propraganda accompanied with illustrations as needed.

How that goes over with the editor is another issue.

Edit: Oh, jeez. I completely misread the question.

[Dag]

Space marines would go back to being brain wiped ex-cons that have been medically experimented on.
The primarchs would go back to being the original space marines rather than the uber creatures that a space marine is 10% of. The references to Nurgle would all go back to being the lord of decay, while only one of the things he is known for is disease. Only in the past few years have they changed his main title to involve disease.
I'd bring in a new side concept into the fluff that perhaps there are chaos influences keeping the man thought to be the emporer alive on his throne.
Chaos dreadnaughts wouldn't be completely sensory deprived between missions.... (there is a difference between being completely insane, and actually being able to fight something.)
Links involving a Tzeenchian plan would be more apparent in the birth of the Tau.
Links involving Dark Eldars servitude to Slaanesh would be more evident... they need the souls to feed to their great enemy....
Chaos wouldn't be focused on chaos space marines... Yes I want to field my Chaos squats! All I hear about are bringing back the squats...forget them, I want my chaos squats! Hmmm, I'm getting derailed here... now I'm going to have to go think up a good excuse to put them into an army.

[mullinstron]

Would you set Necrons back to being soulless drones in the service of Cthulhu?

This for sure!

[Jmaximum]

I would definitely revert the necrons. the implacable, unstoppable, soulless automatons were just scary. Now they have their own cool-aid man, a ronald mcdonald, etc, which is just dumb.

[Roma89q]

I would just want to know what's under Titan that the purifiers must secretly guard, and also if Trazyn really has a primarch or not. Then bring in world peace!

[ZenPaladin]

I would definitely bring back the mystery of chaos. The big four would become the big four thousand. All races that are psychically attuned would have issues with chaos. Chaos ork, chaos Eldar and yes even chaos nids.

The idea would be that the warp in the milky way is just a fusked up place and no race taps it's power with no consequence. The hive mind for example would suffer from unintended and controlled mutation. Spontanious creation of free will and other weird stuff that it had no defense for or understanding off.

Chaos would be something powerful and dark and unknown and not subject to simple codification. Something only the mad and the desperate dared to look into.

Back to the ultimate big bad.

[George Labour]

I'd add the knight worlds back in, as they were depicted in the Titan Legions game.

Back in the good old days when men in giant robots herded dinosaurs for cyborg technotheurgists on distant Mars.

Might also bring back the eldar exodites but only because I really loved the Dinoriders cartoon.

[Brusilov]

Let's see, where to begin... I'd rewrite the confrontation between Horus and the Emperor to have daddy give a good spanking to his spoiled son...

Joking aside, I like most of the fluff the way it is now. I'd simply rewrite the Star Child/Sensei/Illuminati stuff back, just so much fun to toy around these things...

And I'd retcon the Necron fluff to something in between current fluff and their previous incarnation : I like that the C'tan are no longer the head honchos and that the Necrons have some personality and room for personalisation. However I miss the fact that the Necrons fluff used to tie everything together quite nicely : Orks, Eldar, Necrons, Chaos... It was taken to extreme with C'tan shoehorned into everybody's background, from the Void Dragon influencing the Mechanicus to the Deceiver potentially posturing as Cegorach the Laughing God.

However, it was still better than a bunch of angry Tomb Kings of space bent of galactic domination...

And for the record, The Adeptus Mechanicus does innovate, it just takes 500 years of testing and praying to get a new variant of an existing vehicle approved. Read about that in one of the IA books from Forge World.

[Foxhound2delta]

I would bring back some of the loyalist primarchs or even have a chapter come across one of the runaway primarchs to discover they are evil! Better yet I would delve more into the story concerning possibly primarch being held my the Necrons.

[St.Germaine]

I have several things that I'd like to see them take a different tack on but there are two where GW missed the bus completely that I'd fix.

The first is female marines. The only reason that they were excluded with some flat out ridiculous pseudo-scientific statements is that in the early days the GW sculptors could barely handle male figures. The few female figures they produced in those days were beyond horrible. "If we find reasons not to include female figures, maybe we won't have to sculpt them." They missed the boat so badly from a marketing POV.

The second is not including a loyalist fragment of one of the traitor legions from the get-go. The fluff possibilities boggle the mind. Loyal marines trusted by almost none, actually attacked by some. Kept on a very short leash by the High Lords while they prove their loyalty. A chapter almost rabid in their need to redeem their honor, volunteering for the bloodiest campaigns in order to try and prove their worth.

GW may have missed the boat but I've been playing both concepts for almost as long as I've been playing 40K. (just post-2nd edition)