As per all of the comments here: https://answers.atlassian.com/questions/39986944/answers/40347822/comments/43110013

The key concerns for us with the current implementation are:

• It's not possible to use ScriptRunner's JQL functions (or indeed functions from a variety of add ons) to find children of initiatives that meet certain criteria. With a normal link, or even epic link, it is possible to run JQL to find all linked issues where the parent issue meets certain criteria - for enterprise this is absolutely critical.
• It's not possible to update the field via scripts, it's possible to do this for epic links
• It's not possible to use add ons like Structure to build hierarchies as this isn't a real link type

This basically means the current implementation of the field/JQL is only useful if you want to find the epics linked to known parent initiatives, which only works if you have a small set of initiatives to work with - we have thousands, and cannot currently create a background link to use for searching when a "parent link" is created because we can't access the field value via scripts.

Please feel free to contact me if you would like more information about our use cases.