Having mainly done line of business applications my entire life, I have a slightly different take. Jira won because it was not opinionated. You can use it however you want. FogBugz had the philosophy to make bug entry super easy above anything else. Jira will let a manager define new custom fields and make them all compulsory. It perfectly fits how manager at big companies think. FogBugz provides Completion Date Prob…
They set a project delivery date and you just have to hit it. Do you find that this really works out, in practice? Joel has argued[1] that the only schedule worth anything is the one set by the developers themselves. Management can set relative priorities (X is twice as important as Y), but trying to force a faster deadline on the developers is like trying to make your Linux box run faster by renice-ing every process…
So until there is stable consensus among everyone up to even late adopters about how software work should be managed, any opinion built into the tool will end up being an obstacle for users who are still yet to learn agility the hard way.
The real value of an opinionated tool is the opinion itself. And that is something that has to be instilled first. Build a knowledge-base, a following, a community, then make the tool a companion piece.