Question which is bothering me for some time is whether you should have one tool for bug tracking and another one for feature/story planning? Or should you keep bugs and features in one system.
I think the root cause of this issue lies in misunderstanding of ”bug” and “feature” concepts. End users and software developers look at the same things from so different angles that it is almost impossible to have common view. Old popular comics below illustrates this issue pretty well.

Bug vs Feature
Lets first take a look from end user point of view. There should always be the way for user to register his ideas or issues with using the developed system. So what you do, you give him/her access to your issue tracking. If you are running software product company this could be customer forum or community site like GetSatisfaction or UserVoice, where users shout their opinions without risk to be punished.
So far so good. Now software developer gets into the same system and the fight begins. Argues, whether this issue is a bug or feature, is taking off. Users start pushing to put bug fixes into current iteration, developers fight back by calling issues the features and asking to leave those out of the scope. I guess it sounds familiar.
That is why I think it is healthy to keep bug/issue tracking separate from your project planning. Also you can call me psycho, but emotional aspect is very important here. My point: don’t hold dreams (read: features requests) together with problems (read: bugs). When you do release planning it kills the whole motivation of the team when you see that there are 5 times more bugs than new features planned. We, development teams, like to do something new and not just fix the bugs.
Key goal of bug tracking system is to communicate with customer, understand his point of view, document the issue as much as it is needed and then pass it over to development team. Development team can treat this issue in the plan as new functionality. Call it feature, if it makes you happy. It doesn’t matter.
There are also different styles of using bug and task tracking depending on your company/project time. Software product companies that don’t have direct contact with end user can live with one system with no problem.Though, if you are a service provider and all of your project are done for external customers separate bug tracking is almost the must. From my experience in different types of software projects, I like having separate bug tracking anyway. It makes person responsible for tracking bugs to think like a customer, even you don’t have one participating in the project.