If you just mean you want fewer menu commands, then it is enough to remove the unneeded JAR files from your class-path.
If you need to tailor the UI in other ways, the SciJava UI framework provides a starting point for creating alternative UI plugins however you like. Just extend
org.scijava.ui.swing.AbstractSwingUI if you are building a Swing-based UI) and annotate the plugin with
@Plugin(type = UserInterface.class).
Here are a couple of examples:
Swing SDI – Swing-based UI closely modeled after ImageJ 1.x
Legacy – UI plugin which wraps the ImageJ 1.x user interface; this is what ImageJ2 & Fiji currently use by default
And some other rudimentary/unfinished examples:
I wish I had time to finish them, but there are too many other priorities to worry about UIs for the time being.
Lastly, there is also a JavaFX-based interface for ImageJ2 called ImageJFX, currently in alpha, developed by @cmongis. But I believe that interface is not structured as a SciJava UI plugin.