As what my reading goes about this query is when to use LAMP and when J2EE?? For this, many of the Gurus suggested that for mid/small size projects, the best option available is LAMP over J2EE and for bigger enterprise applications, go for J2EE.
I feel that there is no _intrinsic_ limitation or inefficiency if you use one over the other. Other non-technical and semi-technical issues may become more important in deciding your choice (e.g. how comfortable does your client feel about sourcing Perl programming resources? We were forced to use Java instead of Perl in one largish project just because the customer said Java programmers are available at every street corner.) There are many such issues which may affect the final decision, and the list of such issues will be too long to enumerate here. :)
Shuvam