I'm not sure what your complaint is about the cartooniness and ridiculous out of proportion nonsense is.
The story? Sure. I read many of the old codex's's and the little ministories therein were pretty slick, but it would be difficult to manifest all that into a solid story. For example, [nerd moment] when I was 12 I found some supplement Ork book from somewhere between the first and second editions which explained that Orks were a fungus and the Brainboyz of yore were snotlings. That whole concept was ditched for many years and then suddenly brought back. Not that it really matters as the Ork culture(?) is rather simple, but it was a weird change nonetheless. As far as the other races go, there are stories about specific characters and such, but is there an actual time line to all of it? Don't get me wrong, I love those bits, but they all seem to be random snippets of atmosphere rather than a real story line. [/nerd moment]
Or are you referring to the novels? If so, are they any good?
Back to what I was saying about the characters' bizarre proportions. I don't think they're that far off ESPECIALLY with the newer miniatures. Back in the second edition, Orks looked more like green Nazis with squished faces, but now they're all ripped and what not. Or think back to the old Chaos Obliterators. Those things used to be a few pieces of pewter and not too much larger than the average model and now they're close to dreadnought size. The whole look of the game has really changed over the years.
As far as cartooniness... Well Citadel paints were always pretty cartoony.
With that said, I really hope this doesn't play like the typical WoW clone and I hope it's more than Chaos, Marines, and Orks. It'd be pretty badass running around as a Genestealer or swoop around on one of those Dark Eldar Hellion thingies.