If the plugin has action hooks or filters you can make your changes from your theme without modifying the plugin itself.
an action hook:
do_action( 'my_plugin_do_something' );
a filter:
apply_filters( 'my_plugin_filter_something', $something );
If the plugin doesn’t have those where you need them, you could try suggesting them to the author. For example if the author uses Github.com for developing the plugin and you sent a pull request with the suggested changes you’d have a pretty good chance of having the author add your changes to the core code.