I like the tags at the bottom. Its typical for me to also change the tags when I comment on an issue, so having them on the top would require quite a bit of scrolling - especially when there is a lot of comments already.
In fact, the majority of the time I would end up reading at the bottom of a ticket, so having controls there as well is better then at the top.
One idea for that: the header of the issue could just not scroll with the rest of the page, so you can always see what the title of the issue is, it's current tags and the controls on the right.
I agree that having a sidebar was better in the old design, for the new one, I think there is not that many options available per issue to justify the space it would take up.
Instead I would like to see the "Assignee" and "Tags" boxes moved next to the Edit etc buttons. Having them always at the top is more handy, as you don't have to scroll all the way down on longer issue threads.
The close checkbox feels super weird, and I think the GitHub approach to this is better, a "Close and Comment" button next to the "Update Issue" button which should then be changed to just "Comment" since you are not really updating anything, just adding your comment. I am not sure how it works currently, but I expect adding/removing changes to not cause a page reload and being done via JS, so the "Update Issue" text makes even less sense.
In addition to that, being able to assign colors to tags, like GitHub labels, would be a very welcome change.