Theres a few things here.
1.- Massive project where you're not using 75% of the framework.
Let's say i don't want the template engine and the ORM, the framework should let me pull them out. If i need them at some point i'll pull them in. But i know that when i do, these things will be maintained and working.
And this is where a good framework shines. No need to deal with a dependency hell, and you should be able to pull out easily what you don't need.
Edit: If you're just using a 25% of a framework and have no prospects on using it maybe you should look for something smaller
2.- Separate parts stuck on a massive project
Thats not the framework fault but yours. You should write the parts of the application in a way that you can reuse them in another project, using the same framework or in a similar framework with as few changes as possible. And also its part of your work knowing a bit on how the framework works under the hood. The same way an android dev not only needs to know how 'generic' java works, but how android's java vm works.
3.- Those microservices may not follow a standard.
While frameworks allow you to write bad code, they kind of force you to follow some standards which reduce bad code and let other developers take on the project easily.
On the other side, a well developed microservice based project is usually better than an equivalent one that was based up on a framework. But it takes more time/work and has more risks (specially in php).