I know that eAccelerator has this issue. It would be nice if we could utilize it with XML, YML and PHP based mapping though.
Do you know if the same problem would appear with these kinds of mapping strategies?
To give response to your question (eAccelerator and annotations incompatibility), there is a pull request on github, https://github.com/eaccelerator/eaccelerator/issues/19 .
It seems that in the future these could be resolved, and at that time it would be very nice to have that supported with doctrine (symfony2 already has support for this library).
"I just wonder how many users will start thinking of using eAccelerator and then will be facing this huge limitation". Sometimes users just does not have a choice. Imagine the case when you have a hosted site that requires caching functionalities and the only available cache library is eAccelerator (as just in my case). You would be fried as a chicken hehe