The original problem was caused by filters taking precedence over the Faces servlet. Despite filter2 being a filter, it was also associated with a Faces Servlet and as a result executed after all other filters. To counteract that, I associated Faces Servlet with the last filter of my chain, filter3.
With the following mapping both .jsp and .jsf now execute in desired sequence: filter1->filter2->filter3
<filter-mapping>
<filter-name>filter1</filter-name>
<url-pattern>*.jsf</url-pattern>
<url-pattern>*.jsp</url-pattern>
<dispatcher>REQUEST</dispatcher>
</filter-mapping>
<filter-mapping>
<filter-name>filter2</filter-name>
<url-pattern>*.jsp</url-pattern>
<url-pattern>*.jsf</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>filter3</filter-name>
<url-pattern>*.jsp</url-pattern> <!-- only .jsp since .jsf will be picked up by faces servlet/filter combo -->
<dispatcher>REQUEST</dispatcher>
</filter-mapping>
<servlet-mapping>
<servlet-name>Faces Servlet</servlet-name>
<url-pattern>*.jsf</url-pattern>
</servlet-mapping>
<filter-mapping> <!-- this gets picked up last because of filter vs. servlet precedence, not because of position in web.xml -->
<filter-name>filter3</filter-name>
<servlet-name>Faces Servlet</servlet-name>
<dispatcher>FORWARD</dispatcher>
<dispatcher>INCLUDE</dispatcher>
<dispatcher>REQUEST</dispatcher>
<dispatcher>ERROR</dispatcher>
</filter-mapping>