1. (Note, this answer is very much a personal opinion, based on my experience in IT for large corporates) Gantt charts are not a good tool for planning projects based on the information in development tracking systems. They are good for equating planning dates with dependencies, and good for looking at time/cost and scope, but that's not really what issue tracker software is for. They also quickly become too complex and unweildy for medium and large projects. They fail to represent what is really important from an issue tracking point of view because they don't show you the relative sizes of pieces of work. Jira is aimed squarely at Agile, where size IS important, and planning is done at the top level and hence doesn't really lend itself to a Gantt style chart.
That said, I can see many uses for Gantts inside Jira, especially if you're using it for stuff other than issue tracking (and most users do), but the problem I've seen is that it's immensely difficult to define how to do a generic one which would benefit many Jira customers.
2. Yes.
3. I'm not entirely sure on this one. I know that the Agile teams I've worked with simply don't care about milestones - they just use versions for it. The PMs here do some milestone stuff I think, by using special names on versions, and with Greenhopper, it's even easier because you can do version heirarchies, which can be used to highlight milestones. However, I've found everyone I've moved from Trac to Jira has grumbled about milestones being missing for a couple of weeks and then forgotten about it completely.
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