Maybe make the Orks a bit more menacing and make them less obviously a pastiche of WWI Germans.
Not happening; they were drawn over by Warhammer Fantasy, where they also represented a sort of Hun... just not the German type of Hun. It was weird that they decided to make them more militaristic and stereotypically German of the Hogan's Heroes variety and less barbaric and Chavvy, though given the setting it makes sense.
You'd probably need a different writing crew for 2E. The silliness began creeping in after the Rogue Trader days, where they originally had the setting more of a swashbuckling "adventure" style game and never really stopped.
As for the whole Astartes on Sister thing... blame the writers being awkward manchildren that write their horrid fetishes into books (I'm looking at you Goto and your terrible, terrible works involving Slaanesh's stuff). Cortez was written better after the dark days of the early 2000's, though the whole Cat-girl thing was weird as hell. And honestly, the fact that the imperial guard are kind of useless makes sense; they were patterned partially off Return of the Jedi Stormtroopers. The Mechanicus were also very mad science oriented since 3E; I mean, the Fabricator General had that terrible fake German Accent and everything.
The introduction of the Tau as bluemen who became obsessed with old Japanese anime transmissions you guys have to admit was funny, though GW did get into trouble at one point with Sunrise a few times, especially with Farsight being a very obvious Char wannabe.