When building web apps, is the MVC design pattern always best?

I generally believe in MVC. All applications you create are going to contain components of Control, Data and Presentation and the justification for separation makes a lot of sense. One problem I have with MVC is when building "sub-modules" you often require Control logic that get's either duplicated across Controllers, stuffed into Models and reused or Control logic ends up in the View. The best solution I've found to this is Using HMVC style frameworks. Basically you have a hierarchy of Controllers that are portable and each "sub-module" has it's own controller. Once you've already made a large product in MVC it can be a real pain to switch over to an HMVC approach so if you do end up going with MVC look into solutions that supports an HMVC.

MVC is counter-intuitive at times, especially when the application is small. For a single page application, you are better off embedding the script into the page itself or for applications slightly larger in size and scope, there are micro frameworks that let you delegate tasks differently. If you have to expand the application codebase, then MVC is the key. I disagree with the premise that non mvc applications are performant or are difficuly to scale(considering the performance here); you scale a website, not a piece of code or a framework and the extra lookup call is generally optimized by the time your application goes into the web application server.