I think you should keep it simple but flexible. For example I loathe Jira because their model doesn't mesh with how I work at all. I end up trying to map my processes into their tool mostly for reporting.

The things that I would really like to see are:

1. First class support for dependencies. I want to easily see what a particular issue blocks and what blocks it. I want easy buttons to add a blocking issue or a blocked-by issue. (Also make it super easy to create new blockers which is great for breaking down tasks). I would also love a tool that can tell me what I can work on now, where I can make progress. Basically I want to be able to make a search for my open issues which don't have any open blockers.

2. Performance is very important. It can be fake (do everything in the background and confirm when it is done syncing to the server) but I want to dump things down so I remember them and I can sort them out later.

3. Keep everything flexible. For example I see issue types as an anti-pattern as they restrict what you can do. I often transition issues between types in Jira and end up losing half of the info because it isn't allowed in that schema. I want to track an issue of time so and requirements/plans/priority change over time so I need to be able to change everything about the ticket without losing valuable history.

4. Some sort of simple scriptability. I often have a situation where I run ls, grep or some other quick tool to generate a list then want to file issues for all of the results so I can then work my way through them. So I want an easy way to dump these into the bug tracker (probably as blockers of some other issue).

5. An email interface. I work out of my inbox and the ability to read and respond to issues from my inbox is sooooo convenient. Bonus points if I can do actions such as open/close/add blockers with an email response as well.

6. I also think the concept of "projects" is largely a mistake. Issues switch between project or cut across all of the time. I think tags are generally a more flexible option that satisfies most of the use cases. (A really nice approach that I saw was the ability for anyone to create "lists" which were used a lot as tags. So you can have a "project:foobar" list and a "backlog" list and manage those. This is also more flexible because a ticket can be in as many lists as you want.

7. An amazing feature that I have only seen from launchpad is integration with other bug tracker. My work often depends on other projects which run their own issue trackers. It would be amazing if I could depend on external issues just like internal ones.