@"You force me to design my Annotation class is a certain way (for no obvious reason)"
It is a contract of the implementation, nothing more, nothing less. An annotation class must have a single argument array constructor. Would you feel better if there were an interface with such a constructor? Any contract always "forces" you to design your class that implements that contract in a certain way.
@"You don't want the Parser and Reader to be extensible."
They simply are not designed to be inherited right now which simply means we don't care about backwards compatibility with regards to subclasses when changing these classes and we're not documenting and telling people it is a good idea to subclass them. And frankly, inhertiance just to swap out the annotation construction process is a bad idea. It reveals & couples the subclasses to all the details of the parent class even though all they actually want is exchange the construction process. Moreover you would right now need to extend both, the parser and and reader to swap out the construction process. At least the parser would then need to become an (optional) constructor argument of a reader in order not to need to subclass the reader. Inheritance => strong coupling => hard to maintain backwards compatibility.
If there is strong desire to replace the annotation construction process, a factory (method/closure) approach would be much better.
Can you maybe reveal your concrete use-case? That an annotation class must have a single-argument array constructor is not an unreasonable requirement and you're really exaggerating if you're saying that this simple requirement makes the annotation library unusable outside of Doctrine. That is ridiculous. The Symfony Validator component already uses it.
Please try to be more constructive. Neither did you show concrete use-cases nor is your suggested solution a good idea as it is now because it requires 2 classes to be extended plus 1 constructor and 1 method to be overridden just to exchange the annotation construction process. This can surely be done simpler and will be done simpler if there is enough need for this enhancement.