I think it is inevitable that PS's bugtracker will be replaced someday.
phpBugTracker, the current one, hasn't been updated for nearly 2 years and it would be wasted time for the PS team to update it themselves. Though, I do agree that the current problems with the bugtracker could be greatly reduced with a good set of guidelines, so I look forward to reading them if they are still being written.
The bugtracker that I would prefer is
Trac, it is widely used and has an
entire website full of plugins. There is even a
phpBugTracker2TracScript which I imagine might come in handy. It also has a wiki built-in, which may sound useless for bugtracking but would enable the team to move the current PS wiki into the bugtracker to kind of focus the community on the task of bugtracking (like
Edgewall's site). PS's main website could even be moved into the bugtracker, and the forums. This is a game that is in
permanent development so it
makes sense to centre the community around that development.
As a sidenote it would also be a good idea to get
planeshift.org/, it is a non-profit game.