I've previously worked with Weblogic(EJBs and all), and now I am working with WebSphere. Haven't deployed EJBs on Websphere. But, as far as configuration issues are concerned, Weblogic is way ahead of WebSphere. WebSphere uses its excruciatingly slow GUI(yes, Java based) and our team has agreed that this tool itself was enough to bring down our cumulative productivity. There are other ways of configuring WebSphere, but they are not for the novices nor the usual developers. So, ease of administration, Weblogic gains full marks.
We've faced a multitude of problems with JSP cacheing in websphere. It took us a while to figure out that unless we delete all the cache that websphere maintains, and restart the app.server instance(which in itself can take several minutes), this problem can not be solved. Right now, I don't know much about performance and other issues, but my vote goes to weblogic, beyond any hesitation.