If it is a web-app, use Perl/mod_perl/fastcgi/persistent perl, whatever, buy 4 CPU Xeon processors or Sun Ultrasparc Surefire 6-cylinder servers, fill them up with 20 Gb ram each, put them on a fiber network, take away all other latencies, and then compare.
Well, after such an investment in hardware, the $10000 you quote for Websphere isn't so bad.
I've worked with Websphere, and, it being expensive software, it sucked. It sucked a lot. But buying a licence was a lot cheaper than developing something from Perl and CPAN. (CPAN standardized? Come again? If you throw out the crap modules, the joke modules, and the proof-of-concept modules, you're left with a bunch of decent modules, most of which were either not written with each other in mind, or are not thread-safe, don't deal with Unicode well, or make assumptions on the underlaying filesystem. Mind you, there are a lot of goodies on CPAN - but almost all modules on CPAN were written to do a specific task, and weren't written to be part of a large framework).
What is it about Perl that makes inherently unsuitable for the kinds of things for which J2EE is suitable?
Nothing, but you are comparing apples and oranges. Perl is a language. Websphere is an application providing a framework. And quite a different framework than a language plus a collection of modules random programmers uploaded on an archive site the past decade.
But it's easy to proof Perl is suitable to do what Websphere and J2EE are providing: just write it, and upload it on CPAN.