You can actually use wildcards in the excludes property, that is if you're using ant to run the jacoco unit test:
Blockquote
excludes - A list of class names that should be excluded from execution analysis. The list entries are separated by a colon (:) and may use wildcard characters (* and ?). Except for performance optimization or technical corner cases this option is normally not required.
http://www.eclemma.org/jacoco/trunk/doc/ant.html
You can also exclude files from the report generation process using simple ant fileset tasks:
<jacoco:report>
<executiondata>
<file file="jacoco.exec"/>
</executiondata>
<structure name="Example Project">
<classfiles>
<fileset dir="classes"/>
</classfiles>
<sourcefiles encoding="UTF-8">
<fileset dir="src"/>
</sourcefiles>
</structure>
<html destdir="report"/>
</jacoco:report>
You may have to experiment with the two to get the desired results.