When comparing JIRA Agile vs KanbanFlow, the Slant community recommends JIRA Agile for most people. In the question“What are the best online Kanban tools?” JIRA Agile is ranked 11th while KanbanFlow is ranked 15th. The most important reason people chose JIRA Agile is:
You can provide custom workflows for all the different types of issues. For example you can make features go through a flow of "Backlog -> Needs design -> Built -> Needs QA -> done" with bugs going through a different flow. These workflows are very powerful as you can configure them to automatically assign your QA lead when moved into the needs QA state. These features do require some learning curve to set up, but make the tool a lot more efficient to use as things like managing who is assigned to an issue can be automated.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Highly customisable and powerful workflows
You can provide custom workflows for all the different types of issues. For example you can make features go through a flow of "Backlog -> Needs design -> Built -> Needs QA -> done" with bugs going through a different flow. These workflows are very powerful as you can configure them to automatically assign your QA lead when moved into the needs QA state. These features do require some learning curve to set up, but make the tool a lot more efficient to use as things like managing who is assigned to an issue can be automated.
Pro Powerful tools for issue management
Issues in a current sprint are viewed in a Kanban interface. But for the issues not in a sprint Jira provides a compact view with many powerful tools to search and filter the list. You can create custom filters such as "Show me all issues not yet designed that are assigned to me" and a variety of other tools that make dealing with large backlogs easy.
Pro Has App Marketplace for extensions
Pro Helps you focus on what's important
Jira is a truly Agile software as you may concentrate on the active sprint and the tasks you have to do.

Pro Simple & easy interface
The board space is very well used and configurable. User interactions are clear and intuitive.
Pro WIP Limits
Pro Swimlanes
Pro Pomodoro timer
Pro Estimation & time spent

Pro Collaboration features
Any changes you make on the board are instantly available to all members of the team.
Cons
Con Slow to use
Every view switch and action takes a second or two. Doesn't seem too bad when you first start using it, but the UI is complicated enough that you need to manipulate it a lot and all that time adds up.
Con Merely a thin interface to a massive database
Too many configuration details, too confusing, too difficult to search and modify numerous tickets.
Con Email defaults are crazy-bad
The default is seemingly to email everyone on the team every change on every ticket. Which is stupid-bad. It means you get spammed with so much JIRA garbage you miss actual message tagged with your name.
Con Terrible editors barely work
The in-page editor for issues have lots of issues, plus several hacked-together features that barely work with each other. It's nice that you can drag and drop an image, but just try to format inline text as code, or block text as code, or to use the styles, and you'll find several places where things just FAIL.
Con Expensive
User based price model
Con Ancient
Non-reactive interface.
Con You cannot do a search on all boards, so if you have a lot of info on many boards, you have to search one at a time

Con No mobile app
There is a web app for mobile devices but it lacks some features that a native app could offer.
