I am sure that at some point you will hear from
perrin who has a pretty serious background at the highest levels of web application. After discussions here on exactly the same theme I have recently settled on the model you first propose.
Separating the application and presentation may not be as beneficial as you might think, but the more I get into coding my application the more impressed I am by the ability of even a quite modest Apache server with mod_perl, using CGI::Application and HTML::Template. You might, however, gain something by implementing an additional layer to separate business logic and application logic. I have seen this done in one system by having the business logic implemented in SOAP clients and the application logic requesting the data from another machine. If course, this can be implemented on a single machine for development and testing.
This write-up is an excellent example of just what can be achieved. There has been a lot of discussion in the monastery over the last few months, you might want to try a supersearch on various keywoords like "web application" and see what you can find.
Good luck!
jdtoronto
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