From my experience, the benefits you get from an MVC architecture far outweighs its costs and apparent overhead when developing for the web.
For someone starting out with a complex MVC framework, it can be a little daunting to make the extra effort of separating the three layers, and getting a good feel as to what belongs where (some things are obvious, others can be quite border-line and tend to be good topics of discussion). I think this cost pays for itself in the long run, especially if you're expecting your application to grow or to be maintained over a reasonable period of time.
I've had situations where the cost of creating a new API to allow other clients to connect to an existing web application was extremely low, due to good separation of the layers: the business logic wasn't at all connected to the presentation, so it was cake.
In the current MVC framework eco-system I believe your mileage may vary greatly, since the principles are common, but there are alot of differences between, for instance, Zend, Django, RoR and SpringMVC.
If there are truly other good alternatives to this paradigm out there... I'm quite interested in the answers!
Sorry for the slight wall of text!