> huge installed enterprise base
This is more a reason for a consulting shop to pick JEE.
All in all I think the article more describes why one cannot get around JEE for enterprise work. And how JEE is not as terrible as it was.
That last point assumes levels of "terribleness" are well understood by by many.
When it comes to "startup secret weapons" (except maybe for startups that have to tie in with enterprise systems), I think JEE is the last thing that comes to my mind. Even after reading the article.