The big problem with Cake is that it's very opinionated. That of course is also its big strength. By that I mean that Cake is heavily skewed towards certain kinds of apps, namely standard CRUD apps. If your project is CRUD, Cake can be a huge help. If you're trying to do something very different and want a lot of customization, Cake may actually get in the way.
Because it's very opinionated, it may not sit well with you if your opinions differ. When working with Cake, you have to do things the Cake way. That's not to say that you can't extend and customize it, but even when doing so, you'll have to do it the Cake way. The initial learning curve can be quite steep, and you'll need to be somewhat experienced if you want to step outside the Cake boundaries. The flip side of this is that there's usually a very consistent coding style among all Cake projects.
Cake tends to be a more big-boned framework, compared to those that explicitly try to be fat-free. If high-speed performance is your main goal you may have to spend more time tweaking in the end. That's usually offset by faster development times though. That's the double-edged sword of using a lot of automagic.
There's no major deal breaker in Cake. You can do anything you want with it, just as you can with other frameworks. It just lends itself better to some projects than to others.