I can tell you from experience that the MVC model works very well for most websites and web applications. What may seem like extra effort to you now will save you so much time and effort in the long run.
Example: I'm working on a site right now that is going through a total redesign from the user experience view point. A design agency is going to be changing the design of the site for us, and me and my team will be incorporating the changes into our application (it's a complex app and the design agency are just changing the user interface - none of the actual database code or anything like that).
Honestly, I'd estimate the entire thing will take us about 2 days to do when the design comes through. This is because our changes only impact the view part of the MVC - so the models and the controllers do not need to change at all. Our application will look completely redesigned from a user's perspective, but we won't have to touch the underlying database code at all, so it's really easy.
If we had these mammoth php scripts where the html and application logic and database stuff was all just stuck together randomly, we could spend over a month (or longer) working on this redesign. I look at code posted here daily and know for a fact I'd hate it if I had to work with it.
MVC is great. Invest some time and effort into it and things will start falling into place for you