Instead of sending low-quality pages to a different domain than your high-quality pages, I think it would make more sense and be more beneficial to 301 them all to the new domain, except you'd redirect those low-quality pages to either a similar, higher-quality page or to the home page of the website. I don't think there is much value in using two domains in this scenario. If you don't want the pages, they just shouldn't exist on the new domain and should be redirected to better content.
Best posts made by NoahKain
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RE: Domain Transition: Leaving low quality content behind
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RE: Site Structure question?
I think Option B is the right way to go. From a hierarchical standpoint, Option B is much easier to digest, which is beneficial for the user, Google, and your SEO efforts.
For example, your URL bigbangthemes.net/wordpress-themes/wordpress-ticket-system.
I know I am on bigbangthemes.net. I am looking at WordPress themes. I am currently looking at the WordPress ticket system.
In addition, I think it would make sense to incorporate your niches into the URL structure as well. So maybe go with /wordpress-themes/ecommerce or /wordpress-ecommerce-themes/theme-name
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RE: Domain Transition: Leaving low quality content behind
It might be affecting your domain authority, but I would be more worried about those pages negatively affecting your rankings if the large number of pages are creating a poor UX due to a complicated navigation structure or if users are having difficulty finding the content they want. Overall I would say a general rule of thumb should be: does this content serve a purpose and provide value to our visitors? If the answer is no, then I would 301 to a page that provides value. If it's yes, I would keep the page.