I did test performance of PB with number of other data formats (xml, json, default object serialization, hessian, one proprietary one) and libraries (jaxb, fast infoset, hand-written) for data binding task (both reading and writing), but thrift's format(s) was not included. Performance for formats with multiple converters (like xml) had very high variance, from very slow to pretty-darn-fast. Correlation between claims of authors and perceived performance was rather weak. Especially so for packages that made wildest claims.
For what it is worth, I found PB performance to be bit over hyped (usually not by its authors, but others who only know who wrote it). With default settings it did not beat fastest textual xml alternative. With optimized mode (why is this not default?), it was bit faster, comparable with the fastest JSON package. Hessian was rather fast, textual json also. Properietary binary format (no name here, it was company internal) was the slowest. Java object serialization was fast for larger messages, less so for small objects (i.e. high fixed per-operation noverhead).
With PB message size was compact, but given all trade-offs you have to do (data is not self-descriptive: if you lose the schema, you lose data; there are indexes of course, and value types, but from what you have reverse-engineer back to field names if you want), I personally would only choose it for specific use cases -- size-sensitive, closely coupled system where interface/format never (or very very rarely) changes.
My opinion in this is that (a) implementation often matters more than specification (of data format), (b) end-to-end, differences between best-of-breed (for different formats) are usually not big enough to dictate the choice.
That is, you may be better off choosing format+API/lib/framework you like using most (or has best tool support), find best implementation, and see if that works fast enough.
If (and only if!) not, consider next best alternative.
ps. Not sure what EJB3 here would be. Maybe just plain of Java serialization?