I think Jira is in there just because it is the most used tool. Pick and choose any other tool, if the mindset with the new tool is the same, then we are in the same spot.
The point is that all the prescribed rules pushed down the throat of developers. (e.g. You must have a daily stand up. You must have a story that is no bigger than x Points, you must NEVER roll in our out stories into a sprint once it starts.. and the list goes on and on..The rules - no matter how "small" they are, they are still a big barrier to being agile in the truth sense of the word.
The above are only my observation and my thouhgts, your mile may vary.
