I think you haven't explored the debug feature in
eclipse. We can debug both ordinary java programs and
eclipse plug-ins as well. It is comparable to any
other powerful debugger for java.

Just double click a line of code  where you want to put
a breakpoint, and Run-> Debug As ->Run-time workbench.
The execution starts in debug mode.

FYI: More information about eclipse  and its plug-ins
can be found on the eclipse discussion forum at
www.eclipse.org.