The issue type is Improvement but I think this might be a bug because this used to work quite well.
Any skipped tests were listed as such in the Test Report, and the number of skipped tests was represented by a nice yellow color in the Test Result Trend chart. Even now the Test Result still has a column for number of Skipped tests, but it is always set to 0 in each row even when there are skipped tests in the JUnit report.
One theory: this may have started happening to our team after the Performance Plugin was installed, which I think has its own JUnit parser. However, we have this problem even in jobs that aren't using the Performance Plugin.
Update: Skipped tests started showing up again in the Test Result Trend Chart for us again. Please disregard my comment, which should have been logged as a separate, new bug report instead.