Off the top of my head I can give you some general topics I have found lacking in detail and nuance. The LA Times specifically has done a poor job imo on accurately representing some of the opposition to high density developments here in LA.
They also ran this piece [1] on Elon Musk's empire of subsidies which I thought was lacking in context. Disclaimer: I work at SpaceX so I'm obviously biased. There can certainly be criticism of subsidies given to Tesla/SpaceX, but when an article such as this makes no mention of the auto bailouts, or the similar subsidies given to the defense and oil industry I don't find it particularly balanced.
I've also found much of the NY Times reporting on Snowden to push a very national security establishment agenda. My apologies for not being able to give more concrete examples at this time, I hope you understand my statement was made in good faith.
[1] www.latimes.com/business/la-fi-hy-musk-subsidies-20150531-story,amp.html
Not too mention that Maggie Haberman and Mark Liebovich (and probably a few others too that I'm not aware of) can be found in the Podesta emails sending over their articles to the Clinton campaign for review, prior to publication.
Can you reference the source for this? I ask because much of what I've seen between what WikiLeaks tweets and what's actually contained within the email messages is severely taken out of context. (e.g. not understanding what news embargos are [1]) The New York Times were also the ones who originally broke the story of the private email server.
https://wikileaks.org/podesta-emails/emailid/4213
And one of Haberman's stories being sent to Podesta:
https://wikileaks.org/podesta-emails/emailid/51561
Here's a Clinton campaign strategy document that mentions Haberman and how she has "teed up many stories for us before and [we] have never been disappointed":
https://www.documentcloud.org/documents/3125945-Story-Memo.h...
Doing an advanced search on Wikileaks filtering by "nytdirect@nytimes.com" in the sender field, you'll see that the first drafts of nearly 50 different articles were sent to John Podesta:
https://wikileaks.org/podesta-emails/?q=&mfrom=nytdirect%40n...
"Here is the quote that Leibovich is intending to use from your conversation with him unless we see a problem. I don’t."
To quote Glenn "Instapundit" Reynolds, "Just think of the media as Democrat operatives with bylines, and it all makes sense."
I think there are big problems with the way access and coverage are mixed up together and traded on, but I'm pretty comfortable with a journalist agreeing not to publish remarks made during a conversation and then later asking to publish some of them.
[1] http://www.nytimes.com/politics/first-draft/2015/12/23/which...
That Clinton campaign strategy documents comes from, apparently, the Guccifer 2.0 hacks. Glenn Greenwald and Lee Fang contacted Nick Merrill to confirm the document's authenticity, but received no response.
https://theintercept.com/2016/10/09/exclusive-new-email-leak...