I'm gonna go a little all-out on this one - how to make it better
and worse (
imho/
ymmv)!
Black Templar
Why they're cool: They're a bunch of hardcore puritan zealots.
Better: I dunno, they're pretty awesome as they are.
Worse: Turn them into hypocrites. I can actually see this happening if someone with an anti-religion bias takes over the fluff-writing, but
imho the Black Templar are meant to be single-mindedly adherents to their faith.
Blood Angels
Why they're cool: Sanguinius was pretty badass admittedly, and their emphasis on assault and speed is cool.
Better:
Imho, the Blood Angels need a bit more character. Maybe some sort of divide in the chapter and/or successors regarding those who suffer from the Black Rage - some defend them whereas others believe they should be executed immediately. Not sure what I really think about that, but it's an idea anyway (and would open up some new list-making opportunities).
Worse: Play up the "flawless" aspects of the Blood Angels, making them a bunch of even more androgynous pretty boys who are super-special at everything. Start calling every piece of equipment "Blood _____" or "_____ of Blood", etc.
Chaos Daemons
Why they're cool: They're freaking extra-dimensional horrors!
Better: As it is, they don't really seem like that much of a threat to be honest. "Oh no, daemons might attack this world temporarily!" They need some more suitably grim-dark menace to make them seem like a real and terrifying threat (especially considering they are probably the most evil race in the entire game). They should be able to arrive from enemy psykers who suffer a perils of the warp attack (or make it an option instead of a normal perils attack).
Worse: Turn them into cartoonishly evil, mindless monsters.
Chaos Space Marines
Why they're cool: They're Space Marines, only with lots of cool evil toys.
Better: The Legions need to have their flaws played up as if
40k were a Shakespearean tragedy (eg, Thousand Sons need to be more inherently arrogant), and they need to be more of a terrifying foe (eg, successful Black Crusades).
Worse: Make them super-mopey, prone to incessant in-fighting and lose constantly.
Dark Angels
Why they're cool: They... uh... get lots of Terminators. That's cool. Heck, the Fallen are cooler than the Dark Angels themselves.
Better: They need some more differentiating. Not entirely sure how that should be done...
Worse: ...but if they play up the "Lion" angle, that would be the wrong way to do it. Also, making them
justifiably arrogant would be dumb.
Dark Eldar
Why they're cool: They're sadistic, manipulative S&M space elves... that sounds really stupid, but it's awesome in execution.
Better: Hard to say. Personally, I think that Dark Eldar have great fluff currently. I'd maybe play up their mercenary aspects and make their raids seem more threatening, but as they stand they're pretty awesome.
Worse: Turn Dark Eldar into a bunch of moustache-twirling, cackling cartoon villains.
Eldar
Why they're cool: They're psychically powered space elves with a cool caste-like system.
Better: They've been nerfed, fluff-wise. Avatars are a joke, Craftworlds get destroyed every weekend and Farseers are not much more than a plot-device to make bad things happen to the interloping human characters. They need to get back their technological and psychic dominance from humanity (Necrons are justifiably more advanced), whilst playing up their dying race aspect in the process.
Worse: Make it so that they aren't going to die out inevitably. Also, continuing to nerf them in the fluff to the point of obsolescence.
Grey Knights
Why they're cool: They're the elitest of the elite in humanity's armies.
Better: They got pretty derpy in their last Codex... the Grey Knights themselves need to become more rare, acting as tools of Inquisitors. Making them like a super-special Space Marine chapter gets rid of a lot of their mysterious essence.
Worse: Make them all live in the warp with Draigo and launch attacks on the daemons while inside their warp-fortress... Or, at the very least, make all their fluff as cringe-inducing as the 2 pages about Draigo.
Imperial Guard
Why they're cool: They're the expendables, backed up by huge guns.
Better: Guard have pretty awesome fluff as it is. Commanders could perhaps be a bit more colourful though.
Worse: Make them incompetent to the point of redundancy perhaps? I really don't know how you could screw up the Guard.
Necrons
Why they're cool: Space Terminator-mummies.
Better: I personally like their new fluff (before they were just Tyranids with armour plating), but it is far too cartoonish and they lost a lot of their old menace. Maybe get rid of some of the silly aspects of the new Necrons (that map that can blow up solar systems, all of Imhotek's dialogue, Flayed One plague, etc), and make them more evil. Easiest way to do this - make them jealous of the races with flesh-and-blood bodies and/or harvest people for the C'tan again. Retain the new personality of the Necrons though.
Worse: Go back to the old fluff. Yay for flavourless Tyranid rip-off robots.
Orks
Why they're cool: They're hilarious warmongering aliens.
Better: They're already awesome.
Worse: Ditch their humour entirely. That would be crippling. To knock them down even more, make it so they will ally with any race willingly and happily.
Sisters of Battle
Why they're cool: They're nuns with guns!
Better: Sisters revolve entirely around their faith. I'd play up the "Chaos Sisters" element a bit more, but mostly to remind people that it is technically possible (not to make it a common occurrence in the fluff or anything like that).
Worse: See Black Templar entry.
Space Marines
Why they're cool: They're the easy middle-ground army.
Better: Ultramarines are so bland that it hurts. As the poster-boys, they get all of the adaptations as well (the Ultramarines movie, Space Marine game, etc). In my opinion, the blandness of the Ultramarines hurts these products - they're so inherently generic that they reflect poorly on the fantastic
40k universe itself. Ultramarines
need some flavour severely. Bring back Tyrannic War Veterans, make their dogmatic adherence to the Codex more explicit (and with greater consequence) in the fluff, make them force the Codex Astartes onto other chapters (opening up Marine on Marine conflict of interest), etc. Anything is better than "boring".
Worse: Make every Space Marine wish they were boring like the Ultramarines.
Space Wolves
Why they're cool: Freaking space-viking-werewolves. That's

ing awesome.
Better: Take them back to their viking roots and play up individual heroism/sagas, whilst balancing the werewolf aspect without making it overbearing. Change Canis Wolfborn's name so that people will finally shut up about Wolfy McWolferson bull

when they make fun of the Wolves. And make the 13th company more present in the fluff.
Worse: Take some of the stupid bits of fluff (like boarding a void whale and blowing it up) and making all of it like that. Making Wolfy McWolferson the Thunderwolf Rider an actual character.
Tau Empire
Why they're cool: They're a young race with technological superiority.
Better: Honestly, I think the Tau would be better with the rumours of genocide/sterilization.
Worse: Make the manga aspects more explicit by drawing inspiration from more sources. Super Sayan Ethereals anyone?
Tyranids
Why they're cool: They're a swarm of bugs destined to consume everyone.
Better: Personally I don't have a problem with Cruddace's additions to the Nid fluff (burning out from lack of food), as it makes them less over-powered than they previously were. But you know how to make the
40k universe even more frightening? Go with the theories - actually suggest that the Hive Fleets are running away from something... something
big.
Worse: Give the Tyranids an actual weakness. Sure it makes them less retardedly overpowered, but it doesn't fit with a grimdark universe.