Having never actually played DW, my opinion might be less credible. Some of my players in my Rogue Trader campaign, however, have played DW and let me borrow the rule book. I skimmed the book and found that their were many things I didn't like. Now, of course, this doesn't mean that everyone else has to dislike them. But I found that:
1: Solo Mode and Squad Mode
Switching between "modes" is something quite often seen in video games. There, it can work quite well. In a roleplaying game, where the infinite possibilities provide a more realistic setting, I don't see why Astartes don't have access to all their abilities, all the time. Why does joining a squad deny you the features and legacy of your chapter? And why does joining a squad make you deal more damage in melee (circa Furious Charge)? From a roleplaying perspective, there is no difference between Solo and Squad mode other than your character's train of thought. And woeful is the marine who forgets what chapter he is from when he makes a charge with his comrades.
2: Hordes
I don't like hordes because it makes the already abstract rules for combat (because rolling dice is nothing like running someone through) even *more* abstract. While I can understand the necessity of having a way to deal with large masses of weak(er) enemies, I feel it should be more narrative than abstract. I can also appreciate the want for a mechanic however, and the horde rules do work, but I wish they were less abstract.
3: Lack of interesting story
And my *biggest* complaint about DW is the lack of interesting story. If you look at Space Marines as a whole, they are virtually identical. Their only defining characteristics are Chapter, specialty, and past accomplishments. Maybe you are able to work in another character trait or two, but their are still a thousand more marines so similar to you that your only value is as a resource, not a person. Furthermore, Space Marines are very limited in the scope of their goals. As compared to DH and RT, where characters can work to accomplish virtually limitless varieties of missions, DW leaves you saddled with a ball and chain. Your missions will consist of assaulting enemies, assassinating a key enemy figure, defending an objective from enemies, or recovering an objective (read: relic, person, information). Again, creative GMs might be able to come up with something a little different, such as the party being cut off from extraction and having to trek across the continent to reach the extraction point. For the most part however, a player who thinks ahead can prepare for anything the GM can send them.
Now, as I said, I have not actually played DW, so these observations may contain inaccuracies. Or maybe being a Space Marine is enough to overcome these flaws for you. These are just my personal opinions.
However, since being a Space Marine, and consequently awesome, is a natural desire in the 40k universe, my RT players and I did talk at length about what could be done to fix these flaws.
1: Solo Mode and Squad Mode
I would say that the easiest way to fix these is to do away with them altogether. Give Marine's their Chapter's Solo Mode ability all the time, defining them further by their chapters and allowing the aforementioned lack of defining characteristics to define them more from the other characters.
2: Hordes
Since my problem with Hordes mainly consisted of how abstract they were, I would do away with the Horde rules. In large battles, where Horde rules are more necessary and the players aren't alone, I would make the course the battle takes narrative and allow players to influence it with command checks (or if the party was so inclined, use the tabletop game's rules), and allow the players to attack one squad at a time in the standard form of combat. Of course, this does run into problems when its just the players versus a large amount of enemies. I would be personally inclined to use standard combat rules, but still utilize a variation of the rules for breaking hordes. However, since this method does take a lot of time and patience, I can understand GM's accepting the more abstract rules. (and I would be open to suggestions on how to use a less abstract method that didn't take as long)
3: Lack of Interesting Story
Here's the thing. Space Marines are pretty cookie-cutter characters. They all use the same (or similar) tactics. They all have the same organization. They all do what they're told and only think on their own when they can use that brainpower to better accomplish what they're told they have to do. Now, what I have noticed from the novels I've read, the only people that are interesting and have personalities (to some extent) and goals and aspirations (and really, what could be called freedom) are renegades. The Soul Drinkers come to mind first. They are interesting because they have unique mutations and they don't do what they're told, they do what they believe is right. Furthermore, the Soul Drinkers have problems to overcome. Normal space marines are supplied with ammunition, recruits, reinforcements, a home base, et cetera. The Soul Drinkers have to provide all of those things for themselves. And that's just the tip of the iceberg. Fully renegade marines (Chaos) also have their own bickering and politicking to deal with (meaning a marine *might* actually need fellowship or the deceit skill).
So what I'm suggesting is that the only way to make a truly entertaining and unique story is to play non-Loyalist marines. Perhaps they're just marines that have defected and gone mercenary for human pirates and criminals or perhaps they are chaos lords of the traitor legions. Heck, a whole campaign can be built on just getting from the former to the latter and making the moral choices required to get there. Such a path does require a little house ruling of course. I would probably start with the Rogue Trader system and then use DW for character creation, psychic powers, career paths, and equipment. (I would go with RT because its already designed to use powerful characters and because profit factor [or the equivalent] would logically replace requisition. Also, the aspect of owning and operating a ship is a fun aspect that many players enjoy but is harder to use in standard DW)
Keep in mind that these are my personal thoughts and may not work for everyone and I'm not asking them to.