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Is it advisable to enable “Work Item Links” functionality in Jira Align considering the below pros and cons? Also, please share alternate solutions if there are any?
Possible Alternatives to Links:
I counsel teams to avoid using work item links for exactly the reasons you list in the Cons section. Having them in place doesn't necessarily lead to any clearer decisions or actions to be taken.
A team thinking about it's own work should use Story Maps as you suggest. And they can also use the Story Backlog Kanban sprint view to make sure their work is laid out in the best way to deliver what they need. My colleague @Rob Phillips wrote about this here:
If you need to track work between teams (for example, my team needs something from your team in order to complete our work) then that's when Dependencies help. A dependency represents a contract between two teams (whether they be teams in the same Program/Release Train, or across different Programs/Release Trains) to provide something by a needed date or sprint.)
Dependencies show up on the program board and help stakeholders see where there are links between work, and the program board highlights when dependencies are at risk or late. I wrote about building out the Program Board during planning cycles here: