The version of the web.xml is determined when you create a a new Web Project or add Web Capabilities. You are asked for the level of J2EE compatability that you wish to use (1.3 or 1.4). The previous uses the web 2.3 spec and the later uses the web 2.4 spec.
This has nothing to do with the version of JSTL you add, the choice of the web.xml file is made before this.