The Emperors Children have been done very very well in my opinion. Love them or hate them, and I have kinda done both, they have by far the most depth and character to them.
I think people have been basing their judgements on the books legions have appeared in rather than how the legions have been written.
The EC's and the Ultramarines have received the most coverage I think and it's not surprising that the smurfs are close to the top of everyones list, however, I don't feel there has been the same depth of character development as there has been with guys like Lucius, Fabius, Eidelon and others and, because of their 'pursuits' they've also been the legion that has gone through the greatest amount of change from the starting trilogy, through Fulgrim and into Angel Exterminatus where I think they were portrayed superbly as a twisted, perverted legion, the only traitor legion to, imo, really have embraced chaos. I like the fact there has been this huge outrageous progression to an absurd over the top legion, it fits perfectly with manner of their corruption. I really don't like them, but there is a perverse desire to see what characters like Fabius get up to. Have had my fill of Fulgrim though.
The main problem with the Ultramarines is that there is a lot of them and they've not been able to concentrate of particular characters too much, especially when so many have been killed. However, as a legion I think we have been given a very good indication of legion behaviour and mindset. The whole theoretical and practical must surely now be the most established phrase for any legion.
I think the World Eaters were really well done as well, though that was more a really good portrayal of a primark, the best portrayal imo, as Angron wasn't turned against the emperor, he was never for the emperor. I am biased on this because it just so happens that Angrons opinion on the Emperor and the Empire is pretty much exactly my opinion on it and has been since before the heresy books existed.
White Scars - Meh. Don't think they've been done well or poorly. Just very average.
Dark Angels - no real identity with the real big legion issues not being addressed at all and just silly little sub plots that seem unnecessary in telling the story of the heresy - so far.
Iron Warriors - can't remember anything about them, but I do think they did Perturabo well. I do recall them not taking to the Emporers Children which I was pleased about, I didn't want everyone just to full in line and except everything that was going on.
The Thousand sons had I feel two very different portrayals. Their main portrayal was good and gave some depth to the legion, their other portrayal I think was weak, shallow and predictable.
I've not liked the development of the space wolves. They are just too heavily portrayed like Vikings and it just smacks of a lack of imagination to me. Plus there has been too little character development. I actually cant think of any space wolf characters beyond Russ.
Iron Hands. Hmmm. Mixed bag here. Individually they have been portrayed well and I've enjoyed seeing them as the odd survivor here and there joining up with other survivors, however, I do not like this machine over flesh stuff. Interestingly I dislike them just as much as I dislike the emperors children, both because of the path their pursuits of perfection have taken them.
Lunar Wolves were done well. I liked the character development in the trilogy and I am really pleased that Lokien is now a grey knight. However, the Sons of Horus are whiny snivelling turds and that portrayal has wrecked the legion. I really don't want to hear any more about them if they are constantly going to burst in to tears every time horus gets close to danger.
Word Bearers. Individual characters have been done very well though I don't like the portrayal of Lorgar who can topple titans with a fart in the wind and shatters planets when taking a dump. Just stupidly ott. The legion though I think has suffered at the expense of character development. They gone through significant change as well but I couldn't tell you what they are all about beyond thinking their all mini-me's of Erabus.
Salamanders have been giving a good grounding in how they do things, but I also find them boring.
The worst portrayal by far has been the Blood Angels - oh god that was horrible. If I had to use one word to describe the blood angels it would be, camp. Just no no no no no no a thousand times no.
Special mention must go to the Perpetuals. Ole Person has been fantastic. John has been pretty damn decent as well and there is so many places this could all go. I like how they keep popping up to influence events, helps add new twists. However, I was disappointed at the perpetual in Vengeful Spirit (sorry, didn't want to list books but had to be mentioned).