I'm sorry, I didn't read all of the issues (feature request), but I scanned the titles and some content, but didn't find a detailed, comprehensive description, of what i think is missing.

First of all it's a great idea to provide a functionality to embed Links to other nodes (related links). The scanning of article-links and listing of all links below the article is really useful, but... ;o)

1) There should be an option to import links from articles as a weblink-node

2) It should be possible to include links from the directory as related link. If the URL is the same, it gets counted, but there is no auto-completion, search or "this link already exists"-hint.

3) In relation to 2), an "insert link from database"-dialog, like the "Image Assist"-Module (http://drupal.org/project/img_assist), that helps to insert images into content would increase the usability a lot.

4) In relation to 1), an improved administrative-page with a more comprehensive overview of the existing links and differentiation if the link is an "article-link" or a link of a weblink-node would increase the usability of administrative tasks a lot

5) The possibility to differ from link-title and link-description within related links.
Example: Links in posts are often written like this: <a href="domain.tld">click here</a>
The link is added to the "article links" with its title "click here". It would be nice to be able, to define the description in the links-list, for example like this: [link:domain.tld title:Website of Blabla]click here[/link]

6) (less important) Even if there are tagcloud-modules or views-integration, an additional, built-in, more compressed view of the links-catalog could be useful and save time for configuring a view.

If any of these points are realized already and I didn't see it, call me a n00b and please describe how it works ;o)

If there are any questions about these points, simply ask ;o)