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I have some sites with a lot of categories (category, sub-category, sub-subcategory) and locations (country, state/territory, city). To avoid listing pages really deep in my hierarchy I used wildcard subdomains for the locations, but lately I have been told that might be hurting my overall SEO efforts.

I have a lot of URLs like https://city-state-country.example.com on one side of the domain and example.com/category/subcategory/subsubcategory on the other. In the middle you see stuff like city-state-country.example.com/category/subcategory/subsubcategory and everything in between.

Would I be better off moving the locations to the right side of the domain name? Then you might find stuff like example.com/country/state/city/category/subcategory/subsubcategory and everything in between. I think I could do the new rewrite rules fairly easily since every country slug is just two characters long.

I have a couple sites that were penalized by Google for hosting content that made Google look bad. After a major newspaper showcased what was going on they suddenly took a major hit as if someone at Google flipped a switch and told their system not to rank the content for anything other than their brand names. The article made Google look bad because the newspaper highlighted a lot of unverified user generated accusations the reporters assumed not to be true in the context of "these accusations are mostly false, but they still show up on the first page when people search Google."

I was thinking one way to fight this would simply be to host the content at a different domain, but I am concerned about the new domain being penalized as well. I don't want to completely shut down all of the original sites because some of them have brand recognition. The oldest domain is 12 years old with backlinks from several news outlets which is why the content ranked so well, but after the penalty that is only the case on Bing.

I've read various articles about this tactic. Some say that you will almost always pass the penalty to the new domain if you do a 301 redirect, but the penalties at issue in those articles were for things like buying links or other black hat tactics. This is somewhat different in that I wasn't doing anything black hat, they just decided not to let the site rank for political reasons. I was hoping that maybe that type of penalty wouldn't follow it, but right now I am leaning towards simply creating a second site to syndicate articles. It will need to attribute the articles to their sources though, so they will need either no followed links or possibly a redirection script that bots cannot follow.

I would really like it if I could simply change the first site to its .net or .org equivalent and 301 everything though.

@blueprintmarketing it is usually best that these domains are not listed on forums like this one. It tends to take subjects off topic.

I have two sites that were mentioned in a negative article in The New York Times a couple weeks ago. They saw a good increase in traffic, but on the sixth both of them saw sudden unexplained Google drops. Both seemed on the average position from search console doubling overnight.

I run similar websites that have seen no such drops. The only thing these two have in common are being mentioned in the same negative article. Normally I would expect the mention from a major news outlet to make the sites more authoritative in Google's eyes.

Is this a coincidence or a possible manual penalty?

They still rank number one for their respected brand names, but everything else has suffered. Did Google make any recent algorithm changes or do you think someone at Google may have read the article and decided the sites needed to be demoted?