Customization really does need to be deep since it's awfully easy for a faction like Orks to look like each other.

Aye. There are a lot of things to customize your Armor /Weapons. For example the different armor variants or mastercrafted weapons. or even a terminator armor

You are not creating custom Chapters in EC. There are only 4 official Chapters that you can play as.
Hundreds of players can fight on one battlefield in this game. If you allow major color customization, it will be ridiculously difficult to tell who is who in the middle of a hundred+ player battle.

Thousand sons armour or a similar style of armour would be nice to see as a unlock-able armour piece.

Going to be interesting to see how they deal with the customization options for all races.

I hope they won't implement colour customisazion ... since you need to differenciate between chapters/craftworld...

Color schemes are very important I read a comment that said that someone may go paint their chaos marines space marine blue and i could see where in pvp that maybe confusing but customization is really the one way we have to identify ourselves, I am a Dark Angels player always have been but there are 5 or so successor chapters that are completely under utilized this could give voice to the 100's of chapters in the imperium with out a voice. Unless the devs are willing to pump out the several hundred cannon chapter colors. Also my friend a custom color army the theme is his own and the backstory is his allowing a high level of customization would bring immersion into the game and would more then likely increase game play, the more a player is immersed in the game the more he will play (and pay) in the game. As far as Enemy identification goes being able to have a in game identifier over their head would be good, i.e the enemy players name in red instead of blue. Confusion on the battlefield is common sometimes its hard to identify targets that's war. We should not neglect something because it is hard but rise above.

From what I've read elsewhere I don't think the developers are intending to allow chapter colour variations. Lots of other customisation though, armour styles, runes, purity seals, weapon colours etc. Overall I think they'll be enough customisation to satisfy must players. (Think more than space marine but just without all the colour options for armour.)

the stuff like wolf pelts and things should not change stats, they would just look REALLY badass

Are you people paying attention? The Devs already said no outside Chapter/Craftworld/Aspect color schemes. You will not be able to go outside the basic color scheme of the Chapter you are in. That means no creating or "painting" successor chapters because the successor chapters are not participating. At launch it will just be the four chapters and that is it. Customization will come in the forms of gear and Armor pieces but not the basic chapter paint scheme.