Yes, there is an incompatiblity with JSF 2.0 and Tomcat but there is a simple workaround. There are two steps, one that adds the correct JSF libs to your project and one that prepends the correct libs to the tomcat classpath.
Add JSF Capabilities
1. Right-click on your project and select MyEclipse > Add JSF Capabilities
2. Verifiy the values on the dialog and press finish.
Prepend EL Libs
1. Right-click on your Tomcat Server Connector (in the Servers view) and select Configure Server Connector.
2. Expand the MyEclipse Tomcat node and select the Paths node.
3. In the Prepend to classpath box, press the Add JAR/ZIP button
4. Select the el-api 2.2.x.jar and the el-impl-2.2.x jar. You should be able to get the libs from http://search.maven.org.
After you do these two things you should be able to use JSF 2.0 with your tomcat.
As far as the patch goes, we would not typically include a patch with the distribution but if it fixes the problem you are having, then by all means you should install it. It looks like that patch was included in a 2.1 version of webflow and in fact, it looks like webflow is at version 3.0 (I had no idea and couldn’t find that the other day). I’ll log an issue to update our webflow support to 3.0 in our next release if possible.