I work in QA for a startup doing web development. My bosses seem to refuse using a better bug tracking/organizing system. There are some improvements I would suggest for organization.
1. The search function is abysmal. If I search for "cats", it will not also find "cat".
2. If someone leaves the company they are turned into "ghost". That wouldn't be an issue except that you can't search or sort by ghost which means that everything assigned to them now has to be manually searched for.
3. There isn't a good way to make a ticket "in dev" > "in testing" etc. without labels. The labels then inflate since we already have high low etc. Then there are the category labels like performance or customer issue. In the end we have nearly 25 labels and it's almost more of a hindrance.
4. When a new feature is created there are of course a number of issues to fix before it's ready. The best way we've dealt with this is numbering each comment with an issue in it and then having a checklist on the bottom of the ticket that gets checked off. There needs to be some sort of easily view-able checklist which can either be used to indicate completeness of parts of a feature or smaller bugs in the scope of the ticket. It becomes really hard to manage, read, and find reported problems when you have 50+ comments that have bugs in them and another 30 that aren't near their original comment but are related.
5. This might be related to 3 but milestones are also a little limiting. The process we have now is to put something into the current sprint milestone, after it's been validated on a local system we move it to another milestone while we wait for the rest of the tickets. I don't think this is a great way to do this and things should have a status within a milestone.
6. For the love of god do something about the caching. I can go to a ticket where I've made a new comment myself 5 minutes prior, go back to the issues list, and back into that issue and I'm missing several days of comments until I refresh.