Typical web applications don't do a very good job at separating the model, view, and controller logic. The view is particularly confusing as logic is split between server side and client side. This is a side effect from trying to support "dumb" (or nearly dumb) clients (browsers that only support static HTML). Furthermore, logic that would be more appropriate in the model, often gets put into the controller to avoid unnecessary access to the database.
While these design decisions lead to faster web application servers, they also lead to what I call coincidence coding - an unwanted code separation that has no documentation or declared interface. The worst part is that this separation often happens in the most visible part of the system: over HTTP and SQL. This prevents the system from becoming a block box utility, because the internals rear their ugly heads. Any attempt to standardize the protocol (or to use well documented services) is impossible because the protocols get stuck between various components of the view or model and cannot be separated cleanly and maintained across versions.
It is not all doom and gloom: the web is a different place then it was when many of these web frameworks were designed. I am pleased to report that all modern desktop web browsers have good support for client side templating using XSLT (finally!). This means web applications today don't need to support these dumb clients. Furthermore, web proxies have also been improving enough that it is now common for production deployments to plan on use a proxy server in front of the web server(s). Accessing the persisted data is not as much of a problem as it used to be, as database caching is usually planned when systems are being designed.
With these (somewhat) recent developments, its time for a new breed of web frameworks to emerge. These frameworks could implement MVC on the web like we have never seem before - really separating the model from the view and from the controller. This could have a significant impact on the maintainability of web application software.
Yesterday, I introduced what I believe to be the first web application framework that does a decent job of separating MVC. It is called the AliBaba Metadata Server and can be downloaded from OpenRDF.org.
The view logic can only exist in static HTML, JS, CSS, and XSLT files. The model/data is transformed into standard data formats, like RDF and some forms of JSON without model specific transformations. You can't put any model logic into the controller, and all service logic must be put into the model. Stand alone, it would be slower than most web application servers, but with proxy and caching on both ends, I believe it will perform just as well and, most importantly, yield more maintainable web applications.