You might call me cynical, but this is a ranty (and nothing new) list of complaints + FUDs against most web development / application frameworks. Seems like this is also a natural point of transition for believers in another (new) faith, that of self-help (albeit more self deception and vanity all the same).

You fit the bill, rather than the bill fitting you
So many times, it seems that the problem is with MVC as a concept itself. The inherently flat flavor most frameworks put MVC in action to makes it that much more difficult for large codebases. It can't be helped feeling that adopting an MVC design is in many cases, squeezing yourself into a car rather than walking into one.

Something new each time
Frameworks bring in some sanity to PHP (especially), and helps keep silly spaghetti code away. While this is a good thing, this comes at the cost of learning curves of various slopes - which includes familiarizing oneself with a set of code-grammar, APIs, jargon, basic design assumptions, standards, practices and more.

More to get rid of, than keep
I saw @Rasumus tweet sometime that he likes(?) CodeIgniter over others because he has fewer things to remove (CI is pretty light in the first place). Meat is a major factor and there's a limit to how much you can strip a framework before you make it more painful than it originally was.

Complexity? Less or more?
Frameworks add abstraction value, but they add more complexity and might eventually get you to dig the abstraction up all over. Migrating existing code (stuffThatWorksAlready^TM) to fit into a framework / MVC is a sadomasochist affair.

Performance
Sometimes, it feels like you're having a truck do something that takes a bullock cart small car. In the economy, this provides food for a certain class of people who specialize in getting stuff that crawls to stand up and walk. Frameworks can be an overkill for most people who have performance benchmarks to live upto.

The good, the bad, the fugly
CakePHP (good fundaes, personally) leads the race AFAIC. Symfony, CI (Disclaimer: not-so-good fundaes) still lag. Yii shows a huge amount of promise (blogpost coming soon). I've heard much about ZF but I haven't had the opportunity to touch/grope/feel it much. Still, there isn't yet an RoR or a Django in the PHPverse.