Don't have enough reputation yet to to comment a comment, hence another top-level post: Thanks, @fungtional, using something along the lines of

<plugin>
    <artifactId>maven-shade-plugin</artifactId>
    <version>...</version>
    <executions>
        <execution>
            <configuration>
                <transformers combine.children="append">
                    <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                        <resource>
                            META-INF/services/org.flywaydb.core.extensibility.Plugin</resource>
                    </transformer>
                    ...
                </transformers>
                ...
            </configuration>
        </execution>
    </executions>
</plugin>

works like a charm! Would have loved to flag your comment as working solution...