I'll talk mainly about ground combat, because I don't really know enough of the specifics of the space combat to debate accurately in that area. Although, I get the impression that the average Space Marine Destroyer-class (whatever that may be) could probably wipe clean a planet anyway.
Anyway, now for a step by step analysis. I'll be comparing a storm trooper and a space marine.
Base stock:
Star Wars: A clone of a fairly able warrior who has been genetically engineered and trained from birth. As clones, they would probably be able to work together as a team like no other army could.
Warhammer: Your average space marine was already a hero in their own right, before they were inducted, in a process where they are rediculously over-amped, giving them super-human speed, strength, perception, etc. Only about the stronger half of inductees even survive their training.
Armour:
Star Wars: By all evidence, the basic storm trooper armour provides almost no protection. It may suffice to keep the wearer alive from ordinance (explosions going off near them), but otherwise is of little value. Aside from looking cool. And also perhaps some sensory equipment which may help.
Warhammer: A space marine is a walking tank. Also, from what I've heard, the armour is powered and hooked directly into the brain so that it in fact increases movement speed, as well as strength, etc.
Weaponry:
Star Wars: Let us be extremely charitable and assume that if a clone trooper managed to hit a space marine in the torso or head, it would kill them. Which may be fair enough, given it seems to be enough to kill a robot - and they're made of metal. Although, probably not metal anywhere near as thick as what the space marines wear, but still, as I said, I'm being extremely charitable.
Warhammer: A bolter is essentially an automatic weapon firing 100 caliber (or possibly larger) high explosive rounds. If it hits a storm trooper - anywhere - they're going to die.
Scale:
I'm not sure, but I get the impression that the entire imperial clone army might in fact be smaller than one of the larger space marine chapters. And there are a lot of space marine chapters.
So, uh, yeah, storm troopers would get screwed over. Although, I could imagine that the average clone trooper would be noticeably better than an imperial guardsman. But then again, there are way more imperial guardsmen then there are space marines, so...
Also, as cool as Jedi are, I mean, how on earth would one use a lightsabre to block a bolter shell? Also, they're rather low on numbers...
General rant:
Technologically, one might argue that star wars may not be quite as advanced as warhammer 40k, but that they aren't as stagnant. Well, if you ignore KOTOR, which says that 4000 years ago their technology was essentially EXACTLY THE SAME. Nonetheless, I generally get the impression that the Star Wars universe is much more open to progress than the Warhammer universe. Because in the Warhammer universe, progress is generally synonymous with heresy.
So, perhaps give the Star Wars universe 10 000 years, and they might be on better footing with the Warhammer (now 50k) universe. Because in the Warhammer universe, almost nothing ever changes. You know, unless the Star Wars people decide to use that time to have another 3 major governmental collapses or whatever...